Couple of thoughts (for general consumption; Curt and I just chatted via telephony):
1. Bottom paint sucks. It's toxic and nasty. So we avoid using it on small boats as much as possible. But it's the only solution for a boat that lives in the water for long periods...
2. Except to switch to a two-part paint, like Interlux Perfection. This won't degrade after long immersion, at least not as quickly, and freshwater algae can be scrubbed off from time to time. (In salt water it's not a good option.) The downside is that two-part paints are very tricky to work with unless you have a lot of painting experience.
3. If you use bottom paint, it should be applied directly to the sanded epoxy. MAS Epoxy and bottom paint get along well. You might have to use a special primer with some epoxy brands.
4. For small boats that will be in the water longer than a few weeks but less than a few years, I prefer a non-ablative bottom paint. We use Interlux TriLux 33 on PocketShip, Peeler, and Madness-the-proa. Intended for powerboats, it's hard enough not to come off in your hands or on the trailer bunks. It's not as resistant to marine growth, however.
5. I've been using Interlux Brightsides paint below the waterline on small boats since about 1991. It's fine for a small boat's typically short stay in the water. The Eastport Pram I towed behind my cruising sailboat had Brightsides on the bottom. The paint never gave any trouble when kept in the water for as much as a week at a time.
6. It's worth noting that Interlux Brightsides takes a long time to reach full hardness. Once it's really baked onto the boat---after a few months, say---it'll be a lot more durable. I think if you rolled on a few coats below the waterline and put the boat in the water a day later, the immersed paint would start peeling pretty quickly.
7. Single-part paints like Interlux Brightsides and single-part varnishes like Interlux Schooner remain the best choice for amateur boatbuilders who use their light craft in normal ways. We have one of the world's most reliable ongoing product tests in the form of our 80+ boat demo fleet, all of which have Brightsides paint and Schooner varnish on them. Several of the boats live outdoors full time; all of them are abused at demos. They hold up great and still look pretty good at the end of the season---thousands of people saw 20 of the demo boats just last weekend at Canoecopia in Wisconsin. Another interesting data point: Scott Mestrezerat's varnished Kaholo did 2400 miles on the Missouri and the varnish on the bottom looks fine. I know because the board was leaning up against the checkout counter in the booth all weekend.
I hope this thread forestalls hand-wringing about using Brightsides paint and Schooner varnish below the waterline on small boats. You only have to fret about it if you're going to leave the boat in the water continuously for weeks or months at a time.