You should do the primary balancing with the tank empty, as you will want the plane to remain flyable when the fuel supply is exhausted. This means you may be slightly nose-heavy with a full tank; this should cause far fewer problems then ending up tail-heavy.

CG is measured in relation to center of lift, generally reduced to the 30% mean aerodynamic chord of the wing. For a trainer, that's just a little forward of 1/3 of the chord at the root, and usually directly on the main spar.

The chord of the airfoil is the measure from leading edge to traling edge.

For a straight, non-tapered, nonswept wing, the mean aerodynamic chord (MAC) is the same as the chord at any distance from root to tip (anywhere along the spar)

When you taper (change the width of the wing as it progresses from root to tip) or sweep the wing, the MAC changes, and measuring at the root only is incorrect.

If it is a straight swept wing, with no taper, you can closely approximate the MAC at 1/2 the distance from root to tip.

For a tapered and swept wing, there's a complex calculation to get the correct location... Easier done with a drawing and I don't know how to post a picture here. (visit http://webpages.charter.net/rcfu/ he has the method posted, along with a LOT of other useful stuff.)

simplisticly, on the trainer, if it measures 10 inces from leading edge to trailing edge, and the wing has no taper or sweepback (typical) the correct CG location would be appx 3 inches back from the leading edge. (30% of 10 inches.) You will typically find that this is also the high point of the airfoil and the place the spar is located. It would not be incorret to ballance as far forward as 2.5 inches from the leading edge, (for more inherant stablity, and spin resistance) or as far as 3.5 inches back. (for the maximum aerobatic perofromance. NOT good for a beginner!)