@Retro_PiGamer
yes you can have both installed and some wads running on one and some on the other.
i have doom 1 and 2 playing with ir-prdoom sinice i have mp3s for the music. and i have hexen and Heretic running on zdoom.

i have not gotten to running anyother mods yet. still playing with getting the controls down pat first

also look here for more help with running wads with other files.

https://retropie.org.uk/forum/topic/12929/any-doom-mods-recommendations/15

i remembered playing with it before i had to wipe my system