Joe,
Since the motor & ESC says 12V/18A then it would mean the thing is capable of operating from '0'V to 12 V at no more than 18 A. The '0' V thingy is a little rediculous so the low voltage cut-off point is where ever the supplied voltage will run the motor at the required performance. Less than 7.2 volts will work, but that doesn't tell you how well it will work.

Batteries are weight and volume, which means ease in placement in the hull, which also means ballast, which will naturally affect the CG and/or balance of the the thingy. If moving the batteries will result in a better 'balance', then why not? If the boat is only going to turn in one direction then the 'weight' of the boat can be sort of one-sided, sort of. Otherwise, keeping the balance/CG centered, and low, and as light as possible for the particular hull, is a better idea. Which is just a long winded way of saying that if moving the things is possible, and works okay, then do it. The only 'trick' to it is that while you're in the process of finding the best placement, keep your foot out of the throttle (which, depending on the boat and operator, can be a real trick!).
Have fun.
- 'Doc