I run it directly via scripts:
(Host Coop)
#!/bin/bash
/opt/retropie/ports/zdoom/zdoom +set fullscreen 1 -host 2 -warp 01 -skill 2 -iwad /home/pi/RetroPie/roms/ports/doom/doom2.wad -file /home/pi/RetroPie/roms/ports/doom/mod.pk3
or
(Host Deathmatch)
#!/bin/bash
/opt/retropie/ports/zdoom/zdoom +set fullscreen 1 -host 2 -deathmatch......
or
(join)
#!/bin/bash
/opt/retropie/ports/zdoom/zdoom +set fullscreen 1 -iwad /home/pi/RetroPie/roms/ports/doom/doom2.wad -file /home/pi/RetroPie/roms/ports/doom/mod.pk3 -join 192.168.X.X
OR
Check out the Retropie Doom wiki, regarding mods. You could use the same commands above, but put it in /opt/retropie/configs/port/modname/emulators.cfg (that's what the "runcommand .sh " 0 Port" doom" stuff is pointing to...the "doom" directory in /opt/.../configs)
Edit:
(Here are some images I made to dress up the MP scripts)
https://imgur.com/a/C6GCc
Reference: https://zdoom.org/wiki/multiplayer