If, as Fitz mentioned, the boat can be canvased instead of fiberglassed it's a better option (and if you're doing a good job on your glass work, canvasing is somewhat easier and a lot less tedious). Rubber-based stain??? Never heard of it. Are you sure it's not water-based stain - which is available from companies like Minwax? You can use epoxy over both water-based and alcohol-based stains without ruining the adhesion of the resin. Alcohol-based tends to be beautifully transparent where water-based is usually slightly more cloudy but it's somewhat easier to work with because it dries slower.
In either case, the amount of time available to rub it down and even it out is far less than with oil stain, so neat, even application is needed. Alcohol stain dries almost instantly, water-based will yield a couple minutes of rub-out time before it's too late to mess with. Most people get a more uniform application with water-based by building up the color using several diluted coats of stain, rather than trying to do it all in one coat. As long as you keep in mind that you don't have long to work it and need to apply it neatly (no drips on adjacent areas and don't bite off more than you can chew in terms of area covered per brush-full) application is pretty easy. Keep in mind though, that most filler won't absorb stain the same way that wood will. You may find that staining won't hide the fills, but simply makes both the wood and the fills different colors. It's probably worth making some scrap wood test chunks with fills to see whats likely to happen on the real thing.
. I was thinking of using a latex based wood stain before putting on the fiberglass to help hide the filler. Is that going to effect the adhesion of the epoxy at all? Any suggestions?
