Can I epoxy the bulkheads before I install them. It seems that it would be alot easier and a better job to do them on a flat surface instead of upright in the boat.
Will this affect the fillets as to adhearing to the bulkheads? Should I roughup the epoxy along the bottom before filleting?
if you tape off the edges where they mate with hull you should be fine. building up epoxy on the mating surfaces will affect fit and shape of hull enough to make you wish you hadn't, imho. it will cost you a lot of time coating first one side, waiting for cure, then the other. for three layers. personally i wouldn't bother, you'll have plenty of other vertical surfaces to coat.
yes, you'll have to scuff sand the cured epoxy to adhere fillets etc.