Actually with the latest beta you *may* be able to get something to work...
I added a 'rom_folder_subfolders' list_generation_method, which should pick up your roms if used with 'rom_path c:\mame\roms'. As long as you have MAME's mame.ini (rompath) setup to recognise multiple rom paths and have Mamewah's 'emulator_commandline' set to 'c:\mame\mame.exe [name]' (+ any flags you might want) then it should launch the games fine.