Don't get too frustrated over it.
I've tried this more ways than I'd care to go over in detail. Easiest way I find is to adjust your LCA's first if you have larger tires, and get them where you want front to back (upper control arms connected at this point). Then, use the UCA's to center your tires side to side. Usually, you'll leave one arm alone, and as you lengthen and shorten the other, it will move the rear left or right. It's easy on a four post lift, but if you're on the ground on your back, I just spread my arms and use my fingertips to get me in the ballpark, then measure when I think I've got it right.
Once that's done, take a look at the pinion angle. If your rear is a bit off to one side, or control arm mounts aren't dead nuts on, you may have to move one upper control arm in or out more than the other to get the pinion set properly while maintaining your frame rail clearance (we're not talking much here, one or two threads can move the rear a LOT). If its looking like you will have to bring your upper control arms way in to get the correct pinion angle, the lowers may have to be extended some as well, since the tires will start to creep forward.
The hardest part is finding a reference mark to check for square. I've done it from ball joints, best measurement frame centerline set with a laser, etc, and never had any real way of knowing if one was 100% centered. Going from both ball joints and centerline, I've had my diagonals right on the money and off as much as 1/2" difference, and it made zero difference in the way the car launched or tracked for me, so I don't even double check it any more as long as my tire clearance is good and my LCA's are even using factory mounting points and a Currie rear (which I know for a fact the brackets are off slightly.)
If all four links are connected, it probably only takes me 10-15 minutes at this point to get the rear centered and pinion angle set, starting from scratch. You get used to it after the first few times.