I would put something between them. It likely won't hurt anything in the short term, but why wait for a problem. Maybe something as simple as a piece of velcro so the caps don't rub directly on the battery.

Good idea on the velcro Mike, I will definitely do that.
Im getting ready to program the controllers. Do I need to disconect both black BEC jumpers since I only have a UBEC on one of the controllers?
Thanks

For operation, yes. You will need bec power for each controller you program, though.

So do I need to buy another UBEC or once I plug both controllers in to the Y-harness and then plug that in to the receiver, will I be OK?

Only one UBEC is necessary.

So should I program the ESCs with both of them being plugged in to the Y-harness or does it not matter if the esc without the UBEC attached to it is programmed without being tapped in to the Y-harness. (did that make sense? :P: )

Scratch that last post Mike. You actualy answered my question a few posts up. Sorry.

Truthfully, you may even get away without the UBEC. The controllers will share the load of the servos between them (each controller's BEC will only have half the load it normally would).