Ok, I took my working batch file and changed it to what you would need. Requirements:
3 mame folders with the programs (c:\mame\mame.exe, c:\MameVerPlus\mameplus.exe and c:\MameVerNeg\mameneg.exe)
Make a mameother folder in c with 2 romfolders...c:\mameother\MameVerPlus and c:\mameother\MameVerNeg (
also change the rompaths in mameplus.exe and mameneg.exe to the ones made)
Make sure there's only 1 copy of a rom in the 3 folders, meaning...you want 1945 to play in mameplus, so remove 1945.zip in c:\mame\roms and c:\mameother\MameVerNeg
In Mala, first rompath is c:\mame\roms and second rompath would be C:\mameother with "search subfolders" activated
Put the mame.cmd (the batch file) in c:\mame
In Mala the mame executable would be: c:\mame\mame.cmd
update your mala romlist
@echo off
if "%2" == "C:\mameother\MameVerPlus" goto MameVerPlus
if "%2" == "C:\mameother\MameVerNeg" goto MameVerNeg
mame.exe %1
exit
:MameVerPlus
cd ..\MameVerPlus
mameplus.exe %1
exit
:MameVerNeg
cd ..\MameVerNeg
mameneg.exe %1
exit