I mounted downriggers on my 16 cruiser last summer. You can see where I drilled the holes if you look at my photos in the album titled "bottom paint, downriggers, and something..." (Sorry, I forgot how to copy over the photos...) Anyway, I put them as far back as practical. They sort of straddle the line where transom starts (ends?).
I over drilled the holes and then undercut them with a dremel and filled with epoxy. There is a lot of advice on this site on how to do that and why you might want to. There are photos in the album of the underneath showing the painters tape I used to keep the epoxy in and the foam filler in the side walls. I sort of mounted where the foam ended, but I did have to scrape it away a bit on one side.
I also bought some starboard (it is like the thick plastic cutting boards) to use as a backer for added strength. All in all it was pretty easy, even with the extra steps, and they have been rock solid. In fact, I really should be out getting her ready for fishing season. It is pretty much here!
Hope that helps.
Jackie
