Well, I don't have cab lights but I do have a lightbar that I drilled into the roof (temporary mount) and it was kinda difficult to figure when I started, but I'd take a long straight edge, figure out where you want the lights to be, and make sure both sides line up with your measurement.
Figure out the distance from one side of your windshield and roof. Ie 2"x 4" and take a chalk pen, or dry erase marker and mark it.
Mark your measurement, Ie 2" x 4" on the other side.
Take your straight edge, 2x4, string line or other straight thing, and lay it across your roof. Make sure it is lines up on both sides, and double check your measurements. Then place your lights.
Just MAKE DOUBLE SURE YOU MEASURE OFF THE SAME THING otherwise you will end up with a cockeyed finished project.
As far as drilling holes, make sure you use silicone or some other clear sealant on both sides of the hole ie top and bottom. Tighten your bolts as tight as you think you can without damaging something, and install your lights.
You could probably get away with running the wiring above the roof carpet, but that would take more time and look more professional if done right.
Just try to make sure that there are no open holes after you silicone/seal, make sure everythig is tight, and measure twice or three times before you drill. A mock up never hurts either, and I would suggest it so you can get an idea of what it looks like before it's finished.