Thanks for the comment SF. The guy at the boat store actually had a boat out back that he was fixing up where he had done the exact same thing and he walked me through all of the steps on how he did it. It looked pretty good to me...although he didn't say anything about how much sanding and fairing he had to do to get it like that... One thing to note is that my boat is only 5,40 meters (approximately 19') and the deck has no core and pretty much no contours...so I anticipate that this job will be substantially less work than it would be for a boat of a larger size with lots of deck contours. To put it into perspective, it took me about 2 hours to remove all of my deck hardware.
If I had faired the deck well before applying the additional fiberglass would I still have to do so much sanding and fairing afterwards? I did hear that you should normally add additonal layers to the underside, but the access is horrible and I don't think I would ever be able to do a good job working upside down. If I applied the additional fiberglass carefully, would it still be so difficult to get a smooth surface to paint over?