I removed skylight, cleaned channel and put caulking product called 5200 than reembedded skylight. Almost 10 years now no leaks. 5200 available at West Marine.
Errant finger tap posted the previous comment before finishing. Apply the tape to the deck as there should be a clear outline of where the sklight meets the deck. If the skylight is screwed in from below in the forward berth, as my 300 is, you can poke the screws through and the tape will hold them allowing for easier alignment of the skylight from topside.
Never use 5200 on anything that is not a permanent positioned and I place. Life boy caulking and 4200 can be used. Must remove and clean all surfaces for good bonding and seal. Also make sure boat surface is in good shape and does not need repaired before resealing and reapplying..