Balance with gear retracted. The gear will move the CG back when they swing to the rear. You will be little nose heavy when they are down, but that is better than being a little tail heavy when they retract. The change will be very small, and may not really effect the flight characteristics though. There is also a theory, that since the gear are still mounted at forward position, that weight does not move back when retracted. I dont know for sure.
I did find on mine, that once the gear had been retracted, I needed to add a little down trim, but I believe that was due to drag, and not a CG shift. The aircraft is a good flyer, so if you balance conservetivly, you will be OK.
I received an e-mail from the guy with plane this thread was started about, and said he flew his on Sunday with no problems. Said seemed a bit noseheavy, due to 2 12oz tanks full of fuel. That is a lot fuel, so a long flight can change the CG by a large amount.