I used a catalyzed glazing putty, the non catalyzed ones will shrink a lot.
As for painting, the paint will skin over very quickly while you are painting. For a single stage or the clear on a base clear you want to make sure that you shoot a section on one side, then one on the other side, then move back to the first side and repeat. If you just start on one side at the front, work your way to the back, you may find that when you get to the front on the other side that the paint is skinned over. If it is, your over spray will leave a rough, cruddy looking surface on the paint that is skinned over. If you switch back and forth, there is a better chance at keeping a wet edge which, allows the overspray to "burn in" and leave a nice smooth surface. I would paint in two sessions. Paint the bottom on session, let it cure for a week or at least a few days, then flip the boat and paint the top. Make sure you tape off the bottom tightly. You can tape it off to the floor, which works pretty good if you use plastic. Whatever you do, have everything laid out before you start painting. Once you start, you need to move quickly, that is why a helper is good. If you have to stop for 5 minutes to find something, you will loose that wet edge. Its not that hard, you just have to be prepared and don't lolly-gag around!