You always balance with the CG at the WORST it could get durring flight. With a typical trainer, the worst is with an empty tank.

Definition of worst CG (for this discussion) is the CG where you have the least possiblility of maintaining control of the aircraft. If the CG is allowed to get too far back, then the aircraft can become virtually uncontrollable.

Because you can get carried away with having fun flying the model, and might not always land with fuel in the tank, you need to balance models that have the fuel tank ahead of the CG with the tank full. If the fuel tank was behind the CG (and it can be in some pusher type models) then you would balance with it full.

Precision aerobatic models will often have the fuel tank centered on the CG to make it so the airplane responds the same no matter how much fuel is left.

You don't balance a plane differently based on what type landing gear it has. The wheels only matter when they are touching the ground.