Hi,
Did you try to modify the .gpe files that launch Doom? For example, the contents of Doom2.gpe are the following:
#!/bin/sh
./prboom -config prboom.cfg -iwad doom2.wad > prboom.log.txt 2>&1
sync
cd /usr/gp2x/
./gp2xmenu
You can copy this file with another name (like Doom2Foo.gpe) and edit...