In /home/deck/.steam/steam/userdata/[USERID]/600610/local/Merlin.ini I edited prj_bHardwareMouseCursor so it would say. prj_bHardwareMouseCursor = 0;

This is because when you have a controller plugged in the mouse cursor will not display. I wanted to use a steamdeck layout that allowed me to use the trackpads as a virtual mouse as it is much faster than using a controller.

This is not required but improves the experience a lot.