You always check the CG with the fuel tank empty. In most planes the fuel tank is forward or on the CG. A full tank will make the plane a little nose heavy, but easy to fly. When the tank is low, or empty, the balance will be where it should be. If you balance when the tank is full, when it's empty your plane will be tail heavy. Then the following saying comes into play

"A nose heavy plane flys poorly, a tail heavy plane flys once."