You're right that the final changes are made based on the way the plane flies. When I first balance a model, I do it so it balances with the nose slightly down.

Things to do to check your CG in the air are:
Fly inverted and see how much elevator you need to keep the plane from losing altitude. Should be very little.
Fly the plane and pull up 45 degrees. Then roll inverted; the nose of the plane should gently start to fall, over a period of a few seconds. It should not immediately start to drop and level out.