Check your shell to see if it has a honeycomb section in the middle- many do and you don't want to drill through that; drill outside of the thicker honeycomb area. I used Yakima tracks on mine and have been very happy with them so far (except for the anodizing wearing off). They recommend using a small amount if silicon and not a big blob; my brother worked at a bike shop and installed them and said they didn't have any issues with them installed that way so that's what I did (instead of a big blob). Mine's been on for around six years now with no issues and I carry multiple kayaks (including a couple of heavy sea kayaks) as well as a variety of other stuff.
Definitely measure several times before you drill. Tape your area to drill and drill a pilot hole then step up to a larger bit in order to avoid chipping the fiberglass. If you have carpet in the interior of the shell use a drill bit stop (or just wrap tape around the bit) so it only goes through the shell- if it gets into the carpet it'll snag it and start pulling it. A second set of hands will be a big help.
The Yakimas are easy to take on and off- unlock the bases, flip the plate open and lift the rack assembly off. Handy for those longer trips where you don't need to carry anything and want the best mpg possible.
05 Tacoma TRD, SR5, V6, etc
1978 VW Westfalia
2007 Suzuki DRZ400s
Who is the happier man, he who has braved the storm of life and lived or he who has stayed securely on shore and merely existed?
Hunter S Thompson