I would not try staining, I think this would only cause color variations later on. I expect the colors will match by them selves as long as you have similar thicknesses of epoxy and varnish.

> Try adding a little stain to a tiny bit of varnish and see if
> you can darken that area and varnish the rest of the boat with the
> non-stained varnish blending the edges. Do this all at once when you
> go to varnish. You can keep doing this with successive coats until
> it seems right. You're also probably obsessing a bit - like I do.
>