Today I decided to set my ride height on both sides of the truck for a true 25mm on both sides, front and rear and discovered that in order to get my ride height even accross the tub I have to go about three more revolutions on the shock preload collars on the battery side.

Seems to me that even though it looks odd when you look at the shock collars this should be the right way to go as the extra weight on the battery side is a constant throughout the stroke.

So, is this the right way to do it or should I split the difference?

"Proper" way to do it would be to find a way to reduce weight on the battery side or add weight to the RX/ESC side. I remember seeing somewhere back a few bzillion pages that many of the better racers (club and pro) were adding weight to the front left of the truck (I'm guessing in the empty space in front of the transponder mount). I don't think it needed much, but can't recall. 4 scales (1 under each wheel) will tell you exactly how much and when you have it balanced.