I tried this out now and used the Batch file to Auto-Generate .m3us 1.0.0 found in the download section. As I have already imported my games, f.ex. in this case PSX games, I have to do it manually, didn't do it while importing.
It works fine, put multi disc games into a folder called the same as the game, run the batch file and it creates a m3u file inside that folder, in my exapmle Xenogears.m3u. Edit game entry, Launching ROM file to Games\Sony Playstation\Xenogears\Xenogears.m3u, and save. Tried it out and it works fine.
Just for information, I changed my batch file to .pbp files, as all my PSX games are in .pbp format, and not cue/bin.
for /R "%~dp0" %%I in (*.pbp) do for %%J in ("%%~dpI.") do echo %%~nxI>>"%%~dpI%%~nxJ.m3u"