You should have your truck sitting on it's own weight at ride height when taking measurements for angle and when measuring for the new driveshaft. That is where it will ride, and your angles will be most frequently seen. make sure you have opposite angles at the transmission tail shaft and pinion.
If you have 3 degrees down at the trans, you'll want 3 degrees up on the pinion of the rear end (parallel lines).
Here's a cool video that talks about the importance of driveshaft angle and phasing.