You didn't say what kink of stain you used. Some of these water based stains have a polymer base ( like very thin latex paint) this is not good for epoxy adhesion. Mark's Rit Die suggestion was a good one since that is pure water based like water color paint. If your using a pure water base stain you'll be ok. Here's what I would do.

(only a suggestion) I would sand the boat with nothing finer than 100 grit. Final sanding with the grain. Mask the stained strip. Lightly moisten it with a spray bottle. With the boat on it's side, carefully stain it with a small brush. You may even want to thin the stain so no pigment is left on the surface. The moistened wood will disipate the stain like doing a water color wash and give you a more even color . Then glass the boat and don't worry about it. - and never do it again. Staining always creates hassels.

I corrected a few dings in my glass with water colors on top of the glass then varnished over it. Worked pretty good in hiding a bang (white mark) that would no longer wet out.