You must stain before glassing.  Stain does not soak through fiberglass and epoxy very well.  

As to adheasion... If you look on the West and Mas websites they talk about some adheasion tests you can do with stain.  I tested Minwax Gel Stain using the CLC provided MAS epoxy.  After throughly drying, I applied the epoxy over the stain. Then when cured, cut dimond patterns through the epoxy into the wood.  Using packing tape and duct tape I attempted to "pull" the epoxy off of the wood/stain.  It stuck and where it did pull away it was the wood that gave way not the stain to wood bond.  

 I chose Minwax Gel stain becuase West says that in their testing this stain had acceptable adheasion.  It is also, readily avaialbe at Lowes and Home Depot. 

Hope this helps.   

Here:  http://westsystem.com/ss/epoxy-adhesion-over-stains/

I used an oil based stain underneath the epoxy on my first kayak and it was TROUBLE! Definitely check on the capatability. They suggest the use of water based stain under epoxy on this forum. I have not tried that but you will not like the results of your epoxy if you put it on top of an oil based stain.

i was wondering about what kind of trouble you ran into with oil base i used it on my boat and was going to epoxy it tomarow

i was wondering about what kind of trouble you ran into with oil base i used it on my boat and was going to epoxy it tomarow

i was wondering about what kind of trouble you ran into with oil base i used it on my boat and was going to epoxy it tomarow

i was wondering about what kind of trouble you ran into with oil base i used it on my boat and was going to epoxy it tomarow

i was wondering about what kind of trouble you ran into with oil base i used it on my boat and was going to epoxy it tomarow

Oil prevents the epoxy from sticking to the wood.

Oil prevents the epoxy from sticking to the wood.

Oil prevents the epoxy from sticking to the wood.

Oil prevents the epoxy from sticking to the wood.

Oil prevents the epoxy from sticking to the wood.

Salamander,

You should wait at least 3 days before applying your epoxy. If you used Minwax stain, it may take even longer. That stuff is the worst.

Do a test. Apply some of your stain to a scrap piece of the same kind of wood. Let it dry for a few days, apply some epoxy to the scrap and check for adhesion after the epoxy has cured.

Don't apply your epoxy until you're sure it will stick. If the surface feels or smells oily, you should wait. You'll be looking at a huge mess if the epoxy doesn't stick.

Cheers,

Pat

Salamander,  my epoxy hardened. It's not like it just fell off the boat. It stuck but it just 'fisheyed' like crazy and had a zillion 'craters' in the finish. It was a huge pain to sand it smooth because of these 'craters'.

Do a test piece somewhere. If you don't you're going to create a lot of trouble for yourself when it comes to sanding the epoxy smooth in preparation for your paint or varnish.