Seems the best answer has already been hit on. You want your plane to be able to fly stable in all configurations. Therefore, it make sense to evaluate your CG with the gear up and down. You should be aware of the balance behavior in both conditions. From my experience, it's never a good idea to have a tail heavy airplane at flying speeds, landing speeds or anywhere in between. With a tail heavy plane, you're always fighting the plane wanting to pitch to an angle of attack that can result in a stall. Since most models are not powered like 3D aerobats, the propellor alone cannot generate enough thrust to keep the plane flying in such a high alpha attitude. In the end, find a balance point that insures the worst case still errors to the side of nose heavy over tail heavy.

FWIW, It typically doesn't make sense to balance a tank with full fuel as the tank typically sits on or ahead of the balance point. So, the worst case is with an empty tank.