I used the python script by yorkie but changed the following files:

/opt/retropie/config/amiga/emulators.cfg

uae4all="/home/pi/RetroPie/roms/amiga/+Start\ UAE4All.sh"
default="uae4arm"
uae4arm="/home/pi/RetroPie/roms/amiga/+Start\ UAE4Arm.sh %ROM%"

/etc/emulationstation/es_systems.cfg

<extension>.sh .SH .uae</extension>

/home/pi/RetroPie/roms/amiga/+Start UAE4Arm.sh

#!/bin/bash
game="$1"
pushd "/opt/retropie/emulators/uae4arm"
if [[ -z "${game}" ]]; then
./uae4arm
else
./uae4arm -f "${game}"
fi
popd

This allows to start the games directly or start the gui if needed.