I painted the interior before adding the decks, this gives greater access to akward corners. Also if you add hatches the forward and aft areas will have to be painted also and with the deck on access is very limited.

I have done it both ways. It takes a lot of time once the deck is on but can be done. It is so much eaiser to do before attaching the deck. The main consideration, as you suggest, is to keep the painted area protected from epoxy drips, etc. Even if you get some, a little sanding and touch up work does wonders. 

You painted the hatch areas? I was planning on leaving those "raw" - figure they don't need UV protection as the cover will be on 99% of the time. Or am I crazy?

It's so much easier to paint before the decks go on. My method has always been to tape wax paper to the underside of any crossmembers that will be having decks glued on. You catch any dripping epoxy, and the wax paper easily peels off as soon as your done.  Then lie down inside and clean up all the corners with a brush.

You can always cut and tape up a large piece of painters plastic to just lay over the floor too. just a bigger waste of material and a bit more time consuming, but it still works.

Good Luck !!