Stain will not take anywhere you have epoxy because epoxy soaks into wood.  You have to decide how much epoxy-soaked wood you are willing to sand away to get all the epoxy off.  That will leave a depression that must be filled or it will show in your clear finish.  Or just put a bit of trim tape or paint over the epoxy after finishing the deck.

Another option would be to tape off the offending epoxy area(s), leaving a contrasting epoxy-colored strip next to the stained area.  You'd probably have to cut into the deck a bit right at the tape line to keep the stain from seeping under the tape.  You would fill in the cut lines and rest of epoxy design later when glassing the deck.  Practice on a piece (or pieces) of scrap first.

Good luck.

Probably you cannot sand away/remove the epoxy without removing the very thin top layer of the plywood.  I don't know exactly how dark you want to stain the wood but perhaps you could use a small scrap and put on a coat of  epoxy and several coats of varnish.  You'll be surprised how much darker it gets just from the epoxy and varnish.  Also you could contact the epoxy manufacturer and ask if there's any way to darken the epoxy while mixing, before applying it to the hull.

Can't you add some stain (not much) to the epoxy? That would make the epoxied area color similar to the truly stained area. I bet that the strength of the epoxy would be adversely impacted somewhat, but this would be just a covering to the stronger application of epoxy. I never had need to try this, but the logic seems good

Gougeon article on tinting their epoxy:

http://www.westsystem.com/ss/adding-pigments-to-epoxy/

If you decide to stain, be aware of a few potential problems. An oil based stain is likely to interfere with adhesion of epoxy. I would never use it on a kayak. Water or alcohol based dyes are a better choice, but dyes are generally subject to fading in sunlight. Dyes that use metallic pigments are more fade resistant. A UV-blocking varnish can slow, but won't totally stop fading.

Good luck, Pat

Look here:  http://www.westsystem.com/ss/epoxy-adhesion-over-stains/

I used Minwax Gelstain and it worked fine.  After a Summer of paddling it stuck fine on my hatches and combing that I had stained.   I also did the adhesion test as mentioned in the link about and the epoxy ripped the wood off.  

Some of the water based stains may work better and be preattier, but Gelstain is easy to get.