diff --git a/containers/libreportal/frontend/core/setup/css/setup-wizard.css b/containers/libreportal/frontend/core/setup/css/setup-wizard.css
index 8604f06..3c82c30 100755
--- a/containers/libreportal/frontend/core/setup/css/setup-wizard.css
+++ b/containers/libreportal/frontend/core/setup/css/setup-wizard.css
@@ -295,11 +295,7 @@ body.setup-wizard-open {
 
 .setup-field input[type=text],
 .setup-field input[type=email],
-/* The storage default's select is outside .setup-field (it is a row, not a
-   labelled field), so it would otherwise render as a raw native dropdown —
-   white box, wrong font — against the glass panel. Share the styling. */
-.setup-field select,
-.setup-storage-default select {
+.setup-field select {
   width: 100%;
   background: rgba(var(--text-rgb), 0.06);
   border: 1px solid rgba(var(--text-rgb), 0.12);
@@ -316,8 +312,7 @@ body.setup-wizard-open {
 
 .setup-field input[type=text]:focus,
 .setup-field input[type=email]:focus,
-.setup-field select:focus,
-.setup-storage-default select:focus {
+.setup-field select:focus {
   outline: none;
   background: rgba(var(--text-rgb), 0.10);
   border-color: rgba(var(--accent-rgb), 0.55);
@@ -1390,4 +1385,9 @@ body.setup-wizard-open .eo-modal { z-index: 10000; }
   margin-top: 12px;
 }
 .setup-storage-default-label { font-size: 0.92em; opacity: 0.9; }
-.setup-storage-default select { flex: 1; min-width: 180px; }
+/* custom-select.js replaces the native popup (the OS draws that one and
+   ignores our CSS) with a themed button + list. It enhances any
+   select.form-control, so the class is what makes this match the wizard's
+   other dropdowns rather than showing stock white chrome. */
+.setup-storage-default select,
+.setup-storage-default .custom-select { flex: 1; min-width: 180px; }
diff --git a/containers/libreportal/frontend/core/setup/js/setup-wizard.js b/containers/libreportal/frontend/core/setup/js/setup-wizard.js
index 3e6dafe..bbc84af 100755
--- a/containers/libreportal/frontend/core/setup/js/setup-wizard.js
+++ b/containers/libreportal/frontend/core/setup/js/setup-wizard.js
@@ -593,7 +593,7 @@ class SetupWizard {
     box.style.display = '';
     box.innerHTML = `
       <span class="setup-storage-default-label">New apps store their data on</span>
-      <select id="sw-storage-default-select">
+      <select id="sw-storage-default-select" class="form-control">
         ${opts.map(o => `<option value="${this.escapeHtml(o.value)}"${o.value === this.storageDefault ? ' selected' : ''}>${this.escapeHtml(o.label)}</option>`).join('')}
       </select>`;
 
diff --git a/docs/guide/install-and-use.md b/docs/guide/install-and-use.md
index 4330d39..e1292f6 100644
--- a/docs/guide/install-and-use.md
+++ b/docs/guide/install-and-use.md
@@ -26,23 +26,29 @@ login), installs LibrePortal, and prints the WebUI address + a generated passwor
 
 ### Put data where you want it (separate disks, external drives)
 
-**The installer just asks.** If it finds a second drive, it offers it for app
-data before installing anything:
+**The installer just asks.** If it finds another drive, it offers it before
+installing anything — one list, two independent questions:
 
 ```
-Where should app data live?
+Where should LibrePortal keep things?
 
   1)  This disk (default)      911.9G   808.4G free
   2)  /mnt/bigdisk             3.6T     3.6T free
 
-  LibrePortal itself stays on this disk either way — only app data moves.
+LibrePortal itself — settings, database, logs. Around 20 MB, and it stays small.
+Choose [1]:
 
+App data — everything your apps store. This is the one that grows.
 Choose [1]:
 ```
 
+They're separate on purpose. On a desktop you usually only move the second. On
+a small board with an 8 GB eMMC and a USB SSD you move both.
+
 It picks a subdirectory on the drive you choose, never the mount point itself,
-and skips the question entirely when there is nothing else to choose, when you
-passed `--containers-dir`, or when running unattended.
+and skips a question when the matching flag was already passed — or the whole
+thing when there is nothing else to choose, no terminal, or you're running
+unattended.
 
 The three roots below are still there for scripted installs:
 
diff --git a/init.sh b/init.sh
index 6c2cea2..4689a47 100755
--- a/init.sh
+++ b/init.sh
@@ -188,32 +188,38 @@ libreportalDerivePaths() {
 }
 libreportalDerivePaths
 
-# Interactive disk picker for app data.
+# Interactive disk picker, in the shape an OS installer asks it.
 #
-# The --containers-dir flag has existed for a while, but someone running the
-# curl|bash installer never learns it exists — so a box with a 4 TB disk sitting
-# next to a small system SSD quietly put everything on the SSD. This asks, once,
-# in the shape an OS installer asks it.
+# --system-dir/--containers-dir have existed for a while and nobody running the
+# curl|bash installer ever learned they existed, so a box with a 4 TB disk beside
+# a small system SSD quietly put everything on the SSD.
+#
+# Two roots, asked independently, because they are genuinely different choices:
+# the control plane is ~20 MB and never grows, while app data is what becomes
+# terabytes. On a normal desktop only the second matters; on an SBC with a small
+# eMMC and a USB SSD you want both moved. Backups stay on --backups-dir, which
+# is a scripted-install concern rather than a first-run one.
 #
 # Deliberately narrow:
-#   * app data only. The control plane is ~20 MB and never grows; the thing
-#     worth placing is the data. Offering three roots would be three questions
-#     to answer badly.
-#   * skipped entirely when unattended, when --containers-dir was passed, when
-#     there is no TTY, or when there is nothing else to choose. A prompt with
-#     one answer is not a question.
+#   * one disk list, two short questions. Three questions nobody can answer at
+#     that moment is worse than a flag they never see.
 #   * a SUBDIRECTORY on the chosen disk, never its mount point — that keeps the
 #     "root only ever takes an empty directory" rule intact and leaves anything
 #     already on the disk alone.
+#   * candidates exclude anything on the same filesystem as /, since placing
+#     data there gains nothing.
 #
-# Self-contained (findmnt only), like the rest of init.sh: scripts/ is not
+# Skipped when unattended, with no TTY, when the matching flag was already
+# passed, or when the scan finds nothing else — a prompt with one possible
+# answer is not a question. Self-contained (findmnt only): scripts/ is not
 # necessarily loadable this early.
-initPickContainersDir()
+initPickRoots()
 {
     [[ "$init_unattended_mode" == true ]] && return 0
-    [[ -n "${LP_CONTAINERS_DIR_EXPLICIT:-}" ]] && return 0
     [[ -t 0 && -t 1 ]] || return 0
     command -v findmnt >/dev/null 2>&1 || return 0
+    # Nothing left to ask?
+    [[ -n "${LP_SYSTEM_DIR_EXPLICIT:-}" && -n "${LP_CONTAINERS_DIR_EXPLICIT:-}" ]] && return 0
 
     local sys_dev; sys_dev=$(stat -c '%d' -- / 2>/dev/null)
     local -a paths=() labels=()
@@ -239,7 +245,7 @@ initPickContainersDir()
             squashfs|overlay|overlay2|aufs|tmpfs|devtmpfs|ramfs|iso9660|udf|vfat|exfat|ntfs|ntfs3|msdos|fuseblk|"") continue ;;
         esac
         dev=$(stat -c '%d' -- "$target" 2>/dev/null)
-        [[ -n "$dev" && "$dev" == "$sys_dev" ]] && continue   # same disk as / — no gain
+        [[ -n "$dev" && "$dev" == "$sys_dev" ]] && continue
         paths+=("$target")
         labels+=("$(printf '%-24s %-8s %s free' "$target" "${size:-?}" "${avail:-?}")")
     done < <(findmnt -Pno TARGET,SOURCE,FSTYPE,SIZE,AVAIL 2>/dev/null)
@@ -251,7 +257,7 @@ initPickContainersDir()
     root_avail=$(findmnt -no AVAIL --target / 2>/dev/null | tail -1)
 
     echo ""
-    isHeader "Where should app data live?"
+    isHeader "Where should LibrePortal keep things?"
     echo ""
     printf '  %s  %-24s %-8s %s free\n' "1)" "This disk (default)" "${root_size:-?}" "${root_avail:-?}"
     local i
@@ -259,22 +265,43 @@ initPickContainersDir()
         printf '  %s  %s\n' "$((i + 2)))" "${labels[$i]}"
     done
     echo ""
-    echo "  LibrePortal itself stays on this disk either way — only app data moves."
-    echo ""
 
-    local choice=""
-    isQuestion "Choose [1]:"
-    read -r choice
-    echo ""
-    [[ -z "$choice" || "$choice" == "1" ]] && return 0
-    if ! [[ "$choice" =~ ^[0-9]+$ ]] || (( choice < 2 || choice > ${#paths[@]} + 1 )); then
-        isNotice "Not a listed option — using this disk."
-        return 0
+    # Ask for one root. Echoes the chosen mount point on STDOUT, or nothing for
+    # "this disk". Everything the human reads goes to stderr — stdout is the
+    # return channel here, and prompting on it makes the prompt part of the
+    # answer.
+    _initAskDisk() {
+        local prompt="$1" choice=""
+        echo "$prompt" >&2
+        isQuestion "Choose [1]:" >&2
+        read -r choice
+        echo "" >&2
+        [[ -z "$choice" || "$choice" == "1" ]] && return 0
+        if ! [[ "$choice" =~ ^[0-9]+$ ]] || (( choice < 2 || choice > ${#paths[@]} + 1 )); then
+            isNotice "Not a listed option — using this disk." >&2
+            return 0
+        fi
+        printf '%s' "${paths[$((choice - 2))]}"
+    }
+
+    local chosen
+    if [[ -z "${LP_SYSTEM_DIR_EXPLICIT:-}" ]]; then
+        chosen=$(_initAskDisk "LibrePortal itself — settings, database, logs. Around 20 MB, and it stays small.")
+        if [[ -n "$chosen" ]]; then
+            LP_SYSTEM_DIR="${chosen%/}/libreportal-system"
+            isSuccessful "LibrePortal will live in $LP_SYSTEM_DIR"
+        fi
     fi
 
-    local chosen="${paths[$((choice - 2))]}"
-    LP_CONTAINERS_DIR="${chosen%/}/libreportal-containers"
-    isSuccessful "App data will live in $LP_CONTAINERS_DIR"
+    if [[ -z "${LP_CONTAINERS_DIR_EXPLICIT:-}" ]]; then
+        chosen=$(_initAskDisk "App data — everything your apps store. This is the one that grows.")
+        if [[ -n "$chosen" ]]; then
+            LP_CONTAINERS_DIR="${chosen%/}/libreportal-containers"
+            isSuccessful "App data will live in $LP_CONTAINERS_DIR"
+        fi
+    fi
+
+    unset -f _initAskDisk
     return 0
 }
 
@@ -365,7 +392,7 @@ for ((i=1; i<=$#; i++)); do
         # Relocatable roots (=form keeps the single-token shift logic). Validated
         # by libreportalValidatePaths before any folder is created. Can also be set
         # via the LP_*_DIR environment.
-        --system-dir=*)     LP_SYSTEM_DIR="${!i#*=}";     ((init_shift_count++)) ;;
+        --system-dir=*)     LP_SYSTEM_DIR="${!i#*=}";     LP_SYSTEM_DIR_EXPLICIT=1;     ((init_shift_count++)) ;;
         --containers-dir=*) LP_CONTAINERS_DIR="${!i#*=}"; LP_CONTAINERS_DIR_EXPLICIT=1; ((init_shift_count++)) ;;
         --backups-dir=*)    LP_BACKUPS_DIR="${!i#*=}";    ((init_shift_count++)) ;;
         --manager-user=*)   LP_MANAGER_USER="${!i#*=}";   ((init_shift_count++)) ;;
@@ -2000,10 +2027,10 @@ if [[ $EUID -ne 0 ]]; then
 	exit 1
 else
 	if [[ "$param1" == "init" ]]; then
-		# Ask where app data goes before anything is validated or created.
-		# No-op when unattended, when --containers-dir was passed, or when
-		# there is only one possible answer.
-		initPickContainersDir
+		# Ask where things go before anything is validated or created.
+		# No-op when unattended, when the flags were passed, or when there
+		# is only one possible answer.
+		initPickRoots
 		libreportalDerivePaths
 
 		# Validate the chosen install roots before creating/baking anything.