Polyester is just fine - that's the most common resin used in mass production boat building. Epoxy is heavier and costlier and while it's stronger, it really offers no strength benefit in this scenario. That said... poly is smelly and harder to work with. I stopped using poly years ago. Your call - both will fill the bill equally well.
Lee - you may able to clean up those lazy lines with a plastic razor blade - it won't damage the gelcoat so you could hold it at a shallow angle and draw it right down the seam, using your finger as a guide against/along the hatch seam. Then use it in a scraper and get rid of the excess. Might not be perfect - but should be better than it is now (if I'm understanding what you're saying). Or, use the plastic blade to cut a deep V-groove in the existing caulk seam, then get rid of all the excess, then apply a new bead on top to freshen it up.