Battery Question

I'm starting my EV motorcycle conversion and I've already have the Chassis and the Etek RT motor but my question is this:  Is there any difference at all between having *6  12volt batteries and *12  6volt batteries in the bike?  I have limited room and I've got plenty of places to hide extra batteries so the 6volt choice would be nice I just wanna make sure I'm not sacrificing something for it.  Anybody got an answer?

Brian