There should be no difference in where it balances. The balace point will be the same regardless of whether you do it right side up or up side down. It will just be more difficult to do if the CG is above the suspension points you are using to find the balance point. Remember, the CG is a point that represents the center of mass of the model and does not even have to be in or on the model on some of the more strange configurations. Fortunately, on most models it is a point located somewhere in the fuselage on, above or below a line between your two balance points.