To get my two batteries behind the servo tray and under the push rods I did this:

First, I wrapped them in thin foam making sure the leads came out on the same corner. Then I wiggled them through the former behind the servo tray, and yes it is a tight fit but mine went in fairly easily. I put them through on edge with the connecting wires up, then using my fingers, big - chunky -clumsy ones at that, I rotated the batteries to horizontal under the push rods. I also had pre-placed some foam to the rear of the batteries, or in front of the second former to prevent the battery from sliding to the rear. Finished by gluing in a piece of balsa across the top. I've had many flights with this plane and no problem that I can blame on the battery arrangement.

No, connecting the batteries with a Y does not increase the voltage - I'll let one of the battery experts expain that or you can look in the Battery Forum and get additional information.

If I had it to do over again I would try using just one bigger battery, I have since used 1400 mah and think one of these would be a good solution.

I would be VERY RELUCTANT to cut into the rear of the plane, with luck you shouldn't have to.

Good Luck