I went to Rockler and bought some water-base stains, Antique Cherry and Country Pine.  It's easy to use, cleans up nicely.  I stained my pieces in the kitchen, and the spills came right up.  My boat is going to be two-toned, a Matunuck surf kayak.  I went with the design on the CLC page.  I think it is going to be very nice when done.  This stuff is mixed already, no mixing, and goes right on.  I didn't pick up on any fumes, either.  My dishwasher was a drying rack.  I have no stains on anything at all except the boat. 

The Rockler store, "General Finishing" water base stain.  The label is brown with pine trees.  They Antique Cherry is nice, and you can experiment with the intensity by wiping in on and then off.  I used two coats, then sanded and used a third coat after that.  The Country Pine is very pretty.  There are about ten colors to choose from. 

Dawn

I'm not sure of the process you are using to stain. If you are staining after the deck has been completed and sanded then an overall stain will work. But if you are planning on staining individual strips and then assembling them, (ie half strips dark and half light for an alternating pattern) you might run into problems with sanding through the stain into unstained wood during the fairing and finishing process. This would require touch-up staining which would be really tough to get a match and a real pain.

Dawn, did you run into any problems regarding sanding, i.e., when you sanded, did it take color off or did the color penetrate? Thanks for the info.......D

On my practice pieces, using Solar Lux, when I sanded after staining I took off ALL the stain.  My plan is no sanding after staining.  I am using the blue stain over paulownia.

Kim

Sanding will remove the stain. You must first raise the grain of the wood and then do the final sanding. When I did my MC 16.5 I did two thinned out wash coats to raise the grain and then two color coats to get the desired darkness.

http://www.clcboats.com/forum/clcforum/thread/5622.html

denise, I applied two generous coats of the stain, from Rockler, as I mentioned above, and let it dry, not wiping it off.  It dried completely.  Then I lightly sanded with 220 grit sandpaper and applied a final coat of stain with a rag and then wiped it off.  I think it looks very nice now.  I know it will get darker with the epoxy and fiberglass.  The stain penetrated the wood well but some did come off during that last light sanding, which my guy and I thought was a good idea to make the finish look best.  It may not be necessary to do that sanding, but we thought it best.  And the stain is even, no lighter or darker spots.  You might do the stain-and-remove-excess strategy to avoid the stain being darker between the strips, as yours is assembled already.  I like that Antique Pine color, with two coats it looks nice and won't make your darker pieces too dark.