You'll need to install all 4 corners at the same time, you change the geometry of the suspension enough that you can do half and half.
Socks has a good thread on the process of doing a lowering spring install somewhere. It's a good read, and addresses the entire process. Except the adjustments.
I'd advise that you dial the heights in to match the factory pieces, then dial down your drop while they are off the car. It can be a bit of a PITA to change them on the car especially as your are lifting and lowering.
Your toe should be good out of the box, but your camber will be a bit more complicated. That's the part you will need to get the alignment for.