Scott,

If there is a place on your plane to put a level on it, then do so on the bench, to get an idea what it should look like on the balancer.

Depending on the plane, the thrust line (engine shaft) , the wings and stab should be level.
If you use the level on the balancer it will only throw you off because of the weight of it.
After you do your first one it will look pretty obvious to you. Don't get fooled by the shape of the fuselage, sometimes it will look like the nose is down or up when actually the thrustline and wings are level.
After all is said and done, let it be slightly nose heavy and you will be fine.

High wing plane balance right side up... Low wing balance upside down, makes things easier.

I don't think Steve meant anything by his answer, he just didn't elaborate.