Use the lowers to set the wheelbase. If you have adjustable uppers, then use those independently to adjust pinion/caster up front and the rear pinion angle. If you have factor uppers, then those are fixed. You will need to set the lowers to give you a good combination of decent wheelbase and correct caster/pinion. That's why I wouldn't bother with only adjustable lowers. Either go all out, none at all, or adjustable uppers only. Lastly, 1/4" on the lowers will not make a large enough dent in the caster/pinion angle to disrupt anything. I wouldn't worry about that in the slightest. You want to set the lowers so that, when stuffed, the tires are centered in the wells. Once you have that set, then mess with the uppers. Obviously the uppers effect the pinion angles on both ends and the front caster, which is inversely related to the pinion angle (one goes up, the other goes down). Adjusting one will adjust the other so you will need to find a good balance. Generally, pinion angle takes precendence but that can be argued depending on your axle, tire, lift height, etc.