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HI,
Judging by the date on your post, you've probably long since completed the job. However, for future reference - if indeed you are working with mahogany, the best approach is to remove all varnish, sand all the wood smooth and get out as much of the old stain (if any) that you can. The only way to ensure uniformity of color is to bleach out the wood before applying stain. Kleen Strip wood bleach is a two-part system that works great - just follow the directions. And before you ask, yes - you also need to bleach out the new mahogany. Once thats done, use any of the marine type filler stains made by Interlux, Sandusky etc. Their tints are a little different ranging from browns to reds so experiment a little. If you are bleaching out a piece of mahogany that is veneered over marine plywood, be very careful during the sanding process. Veneers tend to be very thin and you could easily sand through the veneer. After the stain is wiped and you are satisfied with the intensity of the color, give it a few days to dry out well before applying varnish. If your boat is trailered and kept indoors, 4-6 coats of varnish will suffice. If kept uncovered and kept in the water, at least 9. If your in a hurry, Epifanes no sand wood finish is great stuff - no sanding between coats and it layers up nicely and flows out nice and flat if you're using a good badger bristle brush. It contains UV inhibitors as well.
Hope this helps anyone else facing the same project.