A good polyurethane top coat should fuel proof everything just fine, regardless of what stain you use. Minwax makes some good spray on and wipe on polyurethane products. I personally prefer the wipe on for furniture projects. I'm not sure how the ply will take a stain either, you may want to test an inside area first. If it absorbs the stain unevenly, use a pre-stain treatment. Also, I prefer oil based stains over water based; they are easier to work with and give better results in my opinion.

It looks like you are using white glue. It will probably be just fine but Titebond wood glue may be a better choice. Titebond-2 might even be a good idea since it is water resistant. This is just my opinion of course.