I was in the same boat a few weeks ago.. However with everyones help and patients on this forum i converted from mamewah to Mala strickly because of the "automatic mapping" in mame. So my advice would be to use MaLa, and get the mapper plugin from fat fingers.
However and still...currently the only issues I'm having with it out side of MAME / more along front end wise / U360 being that it uses USB... I have other game controllers hooked up to my computer and it seems to "override my U360's when plugged in, such as a psone adaptor, and an N64 Adaptoid.. it takes over scrolling my game list etc, makes my U360's useless when those "other devices are plugged in.. but i think thats more of a windows issue.. nothing more..
and the other issue i have with the sofware is with video previews .. some are perfect, others show up looking all messed up.. and some make the software flat out crash. I deleted divx codec, and did a fresh install on xvid currently using HiQ circo's previews which i cant wait till they get finished side note! ;-) I still would like to know on how to create a .log file for MaLa Crashes / video crashes etc.. any one know ?
oh yeah and this link should hopefully help you as it did me :
http://forum.arcadecontrols.com/index.php?topic=74248.0