Any water based paint or stain will do. Poster paint and watercolor paints would work well. I wouldn't use acrylics unless you want some build up and texture. NO OIL BASED PAINT. Paint the last thing before you apply epoxy and glass. Sand the wood surface with 220 grit or finer and have it ready to glass because you can't sand after the art goes on so work clean. SEEYA Jack 

I'd consider painting on paper rather than directly on the wood if you want to put the design under the glass. I have done this with good results using rice paper and very minimalist design. Here is an example of that technique taken to fairly extraordinary limits:

http://www.kayakforum.com/cgi-bin/Building/index.cgi/noframes/read/173676

As Jack mentions, you will want to avoid oil-based pigment for any art that you will glass over. You had better do a test of the paper (if you use paper)  and pigment you want to use. Check the transparency of the paper and to make sure the ink is stable under epoxy. This recent thread discussed the technique of using paper under glass:

http://www.clcboats.com/forum/clcforum/thread/4572.html

Otherwise you could paint the design on top of the glass as part of the final finishing if you were planning to paint the deck anyway. You would get a different look that may be more along the lines of what you are envisioning. Disadvantage is that the art would be more easily scratched or damaged that way.

--

Ogata (eric)