When doing a lateral balance, one would always include the wing in that. Usually lateral balance is taken care of during the build. It would be the last step before covering. After all sanding is complete. One would install everything--radio gear, engine, everything. Then check the lateral balance. Add weight at this point to the frame of the wing--again, toward the tip so less weight is required. It does no good to balance the CG at this point because the covering will throw that off. Then you would cover it, balance the CG, and re-check the lateral to make sure it didnt' move significantly.

Again, one can get away with epoxying weight to the covering, and I have done that before, but I much prefer to find some wood to glue to, and even on the inside of the fuse if possible because it looks cleaner.

If you have to move the battery back further than you can reach, you have two options.

A) make a hatch to access a battery "compartment" in the rear of the fuselage
B) attach the battery to a platform, and attach that platform to a dowell. Then, using the dowel as reach, slide the battery platform back into the rear of the fuselage and secure in place (leaving the dowell attached for later access).
I'm sure there are other methods, but those two I am familiar with first hand.