Battery in the trunk, over the passenger side wheel, serves two purposes. It reduces the weight in the front end by the weight of the battery (30 lbs??), and it puts more weight on the wheel most likely to want to lift during hard acceleration.
Now, it adds to cost a bit, because you have to run a lot longer positive cable to the starter lug, and you generally upsize the diameter of the cable (to 2 or 0 Gage) to account for reistance losses in the longer wire. You also likely have to drill a hole in the trunk somewhere to run the cable, although I have seen them run through the passenger side opening where the body drained when dipped on the assembly line (the ovalish plug/plate on the trunk floor). The cable can also be run inside the car, through the gutter on the passenger side floor. There are a bunch of ways to route the wire, and I have never done it for a street car, so I am sure someone could give better advice on the cleanest, safest routing.
You also need a sealed box vented to the outside to mount it in. Modern batteries don't offgas as much as the older ones, but you still don't want the battery just laying in the trunk.
Me, I think it is a lot of work for a street car, and prefer to keep the battery up front.
As far as the wiring before paint goes, it kind of depends on how you are doing the project. If the interior is not being painted body color, and could be done at home, then paint it at home, then wire. Same way with the underhood; if you're just painting inner fenders black at home, do it and then wire.
Alternatively, if everything is going to be body color and/or painted at the shop, I'd wait to wire. I can't remember what your plans are for the car, I just remember you considering a bunch of different things (do you remember the plan for this week?