Follow the directions, and measure 3 or 4 times and drill once. Mine has been ridden through some horrendous rain and hasn't leaked yet. Used only what came with the kit.
start with very small bit for pilot hole. I taped my spots prior to drilling to avoid any chance of bitslipping. I used a marine grade silicone I happened to have.
I put masking tape down where the four holes were going to be drilled and then marked one hole and drilled it. Then I placed the rack on the bike with that one bolt and checked the marking for the next hole ... repeating this process and only drilling one hole at a time.
I know it took alot longer for me to do it this way, but you only get one chance to do it right. And it turned our perfect.
All the steps outlined above are good advice. Measure many times, drill a small pilot hole first, attach one screw after drilling a hole and triple check the other marked holes to be drilled. I used black RTV to seal. No fuss, no muss. Good luck.