I put a strip of tape right where I want the edge of the fillet to be. Then, depending on the type of rocket, I use gel or 5, 15 or 30 minute epoxy. With a small model rocket, I attach the fin with CYA and put on a small fillet of 5 minute epoxy. The epoxy seeks its own level and dries real sooth. You do have to make a tape "dam" at the ends of the fillet. If you use epoxy gel you don't need a dam. Apply it with a finger, wait until it is partially set in three or so minutes, and smooth with a finger dipped in alcohol. Then peel the tape off and the fillets will be smooth and perfectly defined.
I use CYA/epoxy for all fins. The carpenters glue doesn't seem worthwhile to me. Takes too long to dry, and since it shrinks, fillets can be uneven. CYA/epoxy is just as strong or stronger. I sometimes use polyurethane glue for internal assemlbies, but it expands while drying, so make sure that it won't be visible.