Drilling sheet metal can be a pain. Years ago, at the dealer, the cars came without roof racks and some came without the holes to mount one. I had to mark, drill and mount quite a few over the years. If I had to guess, well over 100 installed.
First you want 2" masking tape. I do all of my marking on that. I use two layers incase something slip's so I don't scratch
If your installing Riv Nuts (crush nuts), you really want the tool for it if your doing more than a couple. There's a technique that uses a bolt and a couple of nuts, it works but can be a pain.
Mark all the holes and set the rack on the vehicle to make sure you measured correctly. If its hard to put up and move around, cover a larger area in tape so you don't scratch.
Depending on the vehicle, your headliner will be between 1-2 inch's below the roof. I drill small pilot holes first, then lay the rack on those and make sure all the holes are good. If you don't own a drill stop (I don't), wrap a tight layer of masking tape around the bit leaving about 1/2 inch of bit sticking out. I normally wrap about 1/2 layer on my bits. If I drill a bunch of holes, it will squish the tape down some. If i dont put enough, I end up having to rewrap it to keep the end short.
Now the fun part, the main holes. I prefer a UNI bit here. If your holes are anywhere near or bigger than 3/8 inch, the hole wont be round and you have a chance of it leaking.
When all the holes are done, I install the Riv Nuts (or whatever your fastening with) with a small amount of RTV or silicon sealer then wipe off the excess when installed.