I would say I subscribe to the general methods outlined in the book I first read on the technique: Kayaks You Can Build, by Ted Moores and Greg Rossel. This is to say carefully tape off all unwanted areas before adding glue to the wood. This seems like a lot of work, but I tend to agree that for every minute you spend taping, you save a minute of sanding and the final product looks a lot cleaner. Generally speaking, since it is darker, the filler will show up in the wood grain even if you sand off the excess.
I first taped off the two seams, putting tape down on top of the stitches. Then I simply filled in the gap with epoxy paste on my gloved finger. Sometimes it’s easier to remove the tape before the epoxy sets, so this is an option. After the epoxy is cured and tape removed, I snip all of the stitches and pull them free. I sand lightly to remove high spots. Then tape the same seams again in order to fill in the spots left by the wire stitches.
No need to sand again now, because it is time to fill in the wire holes. This is considered optional in the kit instructions I have read. Again, it seems tedious, but I still do it to prevent problems down the road. If the holes are not filled, you will get liquid epoxy drips on the other side of the panel when you first laminate the fiberglass cloth. The epoxy drips are much harder to remove than the extruded paste as you can see here below. It also helps prevent trapped air in the hole. Filling the holes does mean more taping.
I drill a hole in a roll of masking tape every two inches or so, not going all the way through the roll since I don’t need that many pieces. The smaller the drill the better. Then I tear off pieces of tape and line up the tape hole with the wire hole. I fill the holes using a plastic stir stick as a small spatula to avoid missing the tape.
Remove tape and once epoxy is cured, use a small scraper on the other side to remove the extruded stuff. Now its time to create fillets on the inside seams. This will allow the fiberglass cloth on the inside to conform the surface without worrying about sharp inside corners (the cloth would pull away and leave air bubbles). This means more taping.
I tape about 3/8” from the edge on both sides and try to trim the tape at the very ends to match the tapered panels. I plan on using hatches in the hull to allow for storage, so I will see the inside and would like it to be reasonably clean. But even if you never see the inside, a second reason for the tape is it helps you form a small and consistent fillet to reduce unnecessary weight. I apply the filler with a small syringe and smooth with my finger.