this is certainly not going to shake up the fly tying world, but i tried a marker i found in that big box department store (or the local big box craft shop should have, possibly in different brand names) that has some good potential to be included in your fly tying arsenal.
its an elmers “painters” marker and was used to add the white part of the eye above. i only bought a white marker for testing and will have to go back and get a black one to finish off the eyes. just dab it on, let it dry, then apply the black. i used a fine point for the white but i will get an extra fine point for the black. after that has fully dried, overcoat with sally hansens. on this sample i simply over coated the head with some head cement. the white paint didnt run off.
some say weatherproof, others say waterproof. your choice.
Prisma Color (Permanent Marker); Burnt Monfilament eyes; Melted Standard Tubing eyes (different colors; looks like they are glowing); Barbell eyes; The new beads also have eyes !!! All kinds of options to get creative with (and the fish really love it) !!!
I usually use stick on eyes then coat the heads with 5 minute epoxy to seal the eyes and make a really durable, nice looking head. Using 5 minute epoxy I only have to manually turn the heads around once or twice before the epoxy sets enough to just set the fly aside to finish drying/curing.
I like your idea for painting on eyes, I’ll have to pick up a couple pens and try it out.
Also check out the fabric paint at your local Wally World or craft store. It comes in small plastic squeeze bottles with very small tips. Once it dries, which is pretty quickly, it is water proof and can be coated with Sally Hanson or other sealer and comes in many different colors. I will check out the paint pens. They look interesting.