As far as actually drilling, start by looking under the deck to make sure you won't hit wires, interior trim, bracing, or bulkheads. Tape off the areas of the feet with masking tape (the yellow kind, not the blue easy-peel stuff). This will protect the gelcoat from scratches and help reduce chipping when drilling. Have a couple people help you hold the tower where you think you want it, and stand back an look at it to see if it looks funny. I've seen some really nice towers look like crap because they were mounted in stupid places. Measure everything several times and make sure everything is plumb and square. Mark where to drill your holes on the masking tape. Drill pilot holes, and run the drill in reverse till you're through the gelcoat.
It's intimidating, but if you're mechanical at all it's an easy job.