Expect a few opinions regarding avoiding the mess, and here's what I've settled on as a good technique-
See if you can hold the porthole/whatever in place, and mask around it. Also mask the porthole/piece.
Once the porthole/whatever is installed, take a popsickle stick and go around the porthole with a popsickle stick to remove the sealant that squished out, wiping off the popsickle stick with a paper towel frequently. Then remove the masking tape before the sealant begins to harden.
I rebedded the deadlights on my Catalina using a kit from Catalina Direct, with enclosed instructions. There was no mention there of roughing up before rebedding...