I posted before that I use abalone shell sprayed with colored lacquer for inlays. When I sand too much and go through the lacquer I use a pen of the same color to touch it up. The first time I tried that the ink from the pen bled into the epoxy as you said. However, the next time I tried carefully blotting the epoxy carefully over the touched-up area and letting it cure, then going with precoating the whole thing or skip the precoat and go right to glassing. This worked fine.

All that said, another thing I have done on guitars is to take the dye and blot it on with a rag almost like a drybrush technique, with the other areas taped off. If you dry brush very carefully in thin layers you can control the bleeding.

I still think you might want to try a nitrocellulose lacquer in a candy color on top of the epoxy rather than dying the wood. Of course if you're wanting to accent the grain like on a nice flamed or quilted maple then dying is certainly better. In fact, I have plans to build a wood surfboard with flamed maple as the stripes down the board, and I want to dye the stripes, so we can learn or screw up together. Please keep us posted on this as I am curious to see how you end up doing it.