Ben,
Epoxy will stain the wood when mixed with a filler. In my experience, the stain will blend back to the surrounding wood, but not completely, once sealed. I can still see slightly darker sections around areas that I have filled. If you don't want to see that ghosting around the fill then you will have to sand it out. It may be tough to do though without sanding dips into your hull.Try feathering the stain's edges. I learned this the hard way and have since seen threads about epoxy staining.They pretty much echoed the same things said here. Just apply the filler judiciously and try to keep it off of surrounding wood. Good luck.

: After doing a final filling of gaps using epoxy and wood flour I've got a few
: spots where the wood surrounding the filled area is slightly darker having
: absorbed some epoxy. My question is whether I should sand this back down
: to bare wood before fiberglassing or will the color blend in once the
: entire area is covered with epoxy. I've scraped back to smooth and sanded
: the entire boat with 100 grit so I'm happy with the shape, just not with
: the color.
: Thanks.