The Atomiswave has 5 buttons in the JAMMA harness. 1,2 and 3 are in the regular JAMMA position, 4 and 5 are in the same place as the D and select buttons in the MVS. So if you have a cab or supergun with this 5 buttons wired you won't have any problem.
So far no AW game requires more than 5 buttons. If there was ever gonna be a game that requires more (which I doubt), most likely the additional buttons would need to be wired in a special cart that would come with the game, that is inserted in the I/O expansion bay. I think that in games with more than 2 players, the aditional players are wired like this as well. So with this games you would need some sort of kick harness.