Dave,
The lateral balance should be checked with the plane assembled. Don't try to balance the wing by itself.
I have only built two kits, so I'm no expert. I built them like ARFS. Covered everything before attaching the tail feathers. Balancing had to be done after final assembly.
In RCKen's build thread of an LT-40, he describes his method of assembling the whole plane and balancing it before covering.
http://www.rcuniverse.com/forum/fwd....sageID=3439708
After it's covered and ready to fly, recheck balance and make any final adjustments.