Is that high-build epoxy you're talking about? If it is, be careful. If you put it onto timber that's going to swell, move, shrink etc., then the high-build will crack up. If all your timber is absolutely stable, then, make sure it's really dry and clean, paint it with neat epoxy resin then put on the high-build once the resin has gone off - do it within a day at the most to get a chemical bond otherwise you'll have to roughen it up to key in the high-build. If it's not epoxy high-build that you're talking about, then what is it? If you're painting below the water line on the outside, then you really need to get most of the old antifoul off rather than trying to smooth it all out with gunk. You'll be glad you did in the long run. Once smooth, then use a primer that'll go over remaining old antifoul - I used a Jotun product that has aluminium in it - sorry, don't recall the name, and I'm not sure I'd use it again. It was silver and quite thick but I wasn't happy with its performance after the boat went back into the water - the primer seemed to let go in too many places. This was probably due to the timber swelling after three years out of the water. It's easy enough to find a good, all-purpose marine primer but make sure that it's one that's made to go over old paint remains etc., unless you're planning to take the hull right back to bare timber. Also check to see that it can flex a bit. I've since used a different primer and antifoul system that again, sorry, I can't remember the name of but it's an Australian product anyway that's probably not available in the US.
Sanding all the old antifoul right off is a horrible task but if you are actually going to paint the hull with an epoxy finish, then that's what you'll have to do. I have seen it done on a clinker Folkboat and it has held up really well for quite a few years but it's a really big job. If I was doing our boat again though, that's what I'd be doing, simply because it works so well. Our boat though, and the one that I know of with the epoxy finish, are built with plywood planking and all laps are glued with resorcinol. If your boat doesn't have glued laps, I wouldn't even think about using an epoxy finish. It's highly likely that it'll crack up. Why didn't the other boat's finish crack up when it was put back in the water? Probably because the epoxy finish sealed the hull too well. It's possible, of course, that, if this is actually the case, then down the track, as the epoxy does crack a bit, which it must eventually, then the swelling timber will crack it more. We'll see! Rick