I have my MAME arcade ROMs D:\mame_roms\ folder and all MESS machines in d:\mess_roms\ All software list games are in sub-folders of the \mess_roms\ folder as I like to keep them separate from the arcade ROMs.
the software lists must be placed in sub-folders named the same as their software list names
Atari 2600 ROMs must be in a2600 sub-folder (d:\mess_roms\a2600\) MSX 1 cartridge must be in msx_cart sub-folder (d:\mess_roms\msx1_cart\)
You do NOT need to define the softlist sub-folders in mame.ini, only the main folders. I have mine like this.