: The dye once applied to areas with wood flour and bare wood will soak into the bare wood and not into the epoxied areas and so you'll see a color difference. I don't know how extensive your fill areas are so just use your judgement and decide if you can live with it .
If you want try some test panels, by now you should have plenty of short strips to glue up. Fill some small areas on your test strips with epoxy goop, sand to a point your yak is now and apply some stain. Play around and see how you can effect the tenting of it.
I don't know if you have a design on your deck but now might be a good time to make one. I'm about at the same stage you are in building my yak so I can relate to what you are looking at. Good luck!