I just completed all 8 adjustable control arms on my Rubicon. I was told by Clayton Off Road that on the front, the lowers control the wheelbase length and the front uppers are used for the pinion angle.
Assuming you have adjustable front uppers and lowers, the front lowers will set the position of your axle under your Jeep and the front uppers will dictate your "caster". This should NOT be confused with pinion angle as up front, proper caster needs to take precedence over pinion angle or else you will have a Jeep that handles poorly.
On the rear is opposite. The uppers control the position of the axle (wheelbase length) and the lowers adjust pinion angle.
I really doubt this is what they would have said and if this is how you took it, I should point out that it's completely wrong. Just like up front, your lower control arms primary purpose is to set the position of your axle under your Jeep. The rear uppers are used to set the pinion angle and here, you NEED to have it set in line with your drive shaft assuming you have an aftermarket u-joint style one with a double cardan.
Anyways, im happy with the way it came out and I was able to push the front axle forward more and the rear axle back a bit. Jeep definitely handles better.
On a lifted Jeep, you most likely just repositioned your axles under your Jeep back to where they would have been stock. If you went more than that, you would have issues with your coils and experience rubbing of components.