hatch rebedding

I had all intentions on using butyl tape to re-bed the hatches, but during removal, some of the gelcoat pulled up. What is the best way to deal with this situation? Do I need to patch this with something before attempting to re-bed? Should I just use caulk style and try to get a good bead around...

I have done a lot of research and I found some good posts on here - what I am not sure if how to remove the hatch. I opened the hatch and removed about 10 screws from the deck - they were drilled in vertically. I think see 4 screws that are drilled in horizontally. The 4 screws aren't going...