If you use a pre-stain sealer, the wood will absorb the stain much more evenly than otherwise, and this will also cut down on the amount of bleed that you may have under a taped design. The stain sealers are generally used with heavier grained wood such as pine, where staining really enhances the natural grain pattern, but in this application it can help you get the nice clean edges you are after.
I'm not sure how it might affect adhesion of the epoxy, although being water based like the stains you should use, it's probably not an issue. Like everything else, a test panel is probably advisable.
I'll be testing and using this when I stain panels for my Merganser I'm starting on.