DDR2 Controller controlling 4-chips

If the two banks are intended to operate independantly, either different addresses or R/W direction, you need two separate controllers, if they are working fully parallel, you can use a single controller with double data width.

P.S.: My above answer is wrong regarding your hardware. The two banks could be operated from one controller only if they would share the address and control pins. There is no option in the controller IP to split these signals to two physical pins. So you have to use two controller instances in any case.