The Sonex video tips at http://www.eaavideo.org/video.aspx?v=870261092001 shows how to make small fillets using epoxy putty. I decided to give it a try on the new lower cowling lip.
I sanded/smoothed the epoxy/filler and applied a few coats of Rust-Oleum 250704 "Gloss Lobster Red" enamel to the cowling. Image 1 shows the putty (gray) with some Bondo "Glazing & Spot Putty" filler (pink). Image 2 shows the lower cowling fillet after painting.
I could use this filler method for the small intersections of the empennage with the fuselage.