Brandon, I'll jump in here to offer some peace of mind.

It is perfectly acceptable to balance a low wing airplane upside down. It's called pendulum effect. It's much easier to balance an item with it's mass below the pivot point than above it.

You can even use this method to balance the model laterally. By resting the model on the tip of the fin, lift the model by the crankshaft and see which wing (or side of the plane) is heavier. Add weight to the other side.

I've been milking this thread for info and improvments for well over a year. Generally, it's just modelers passing on their experience. I just thought, hearing a second "voice" would be reassuring.

Good Luck!