Of course... before I didn't understand well your problem... the games supported through the default .ini file are:
Doom1, Doom2, Doom TNT, Doom Plutonia, Freedoom, Heretic, Hexen, Strife, Chex, Chex 2, Chex3, UrbanBrawl and Harmony...
Obviously, for different WADs, the .ini file needs to be modified... I'm sorry, I tested ZDoom only with "default" games and I didn't make a custom version of zdoom.ini, maybe other users will be able to help you!