The official Qubes OS faq entry only covers how to change the layout globally - ie. both for dom0 and VMs, with a single layout.
This document shows several ways of using multiple keyboard layouts and being able to quickly switch between them.
Run setxkbmap in each VM. Dom0 stays untouched (running setxkbmap in dom0 too will interfere with the VM's setxkbmap setup).
For instance the following command would alternate between the US English and the Bulgarian phonetic layout when pressing both shift keys:
setxkbmap -layout "us,bg(phonetic)" -option "grp:shifts_toggle"
To automatically run the setxkbmap command when the VM starts, add a /etc/xdg/autostart/setxkbmap.desktop file in the VM's template with the following content:
[Desktop Entry]
Name=Configure multiple keyboard layouts
Exec=setxkbmap -layout "us,bg(phonetic)" -option "grp:shifts_toggle"
Terminal=true
Type=Application
Note: for some reason, with Terminal=false the setxkbmap settings aren't applied until one runs setxkbmap without options in a terminal. Setting Terminal=true works around this problem, but you will notice a terminal flicker at startup.
If you prefer to have a per-vm setup rather than per-template, create a /rw/config/setxkbmap.desktop with the same content as above and add the following line to /rw/config/rc.local:
cp /rw/config/setxkbmap.desktop /etc/xdg/autostart
Note: the reason we can't put the setxkbmap command in the rc.local script is because the X server isn't running when rc.local is executed.
Alternatively, you could add the setxkbmap command to your profile's .bashrc file if you use terminals to start applications.
qvm-run vname 'setxkbmap ...', where the VM is the one whose window is under the mouse pointer (using xprop -id $(xdotool getactivewindow) ). An advantage is that it doesn't require tweaking VMs or templates, but this is a bit convoluted and qvm-run is sometimes slow when the system is under heavy I/O usage, so the layout switch doesn't happen immediately which is annoying.setxkbmap only in dom0. This isn't optimal because:setxkbmap. It is not clear however if this solution won't have the same issues as above.localectl: it's a no-go as it requires a reboot