I have a very similar setup to you .. the 2 x 4000 mAH Nanos. Where are you planning on putting your flight controller? I intend putting it in the bay nearest the motor.
I found that with the batteries in the location that you used the COG was well forward. I cut a battery width slot in one side of the main bay - about 1 inch deep and then hinged this. Once this is in place the batteries can be slipped in sideways and then moved to the back of the main bay .. so you have 2 batteries sideways on. This gave me lots of leeway for changing the COG.