From what I understand, aniline dye is the way to go ... there could be adhesion problems with stain. I have recently glassed the canoe I am building, having dyed the hull with Lee Valley dyes ....the trick is to use lotsa thin coats and build up the colour gradually.

there is a fantastic source of information on this matter at Martin Step's site, Green Valley Boat works. His builders corner has a page on the use of dyes "http://www.greenval.com/FAQstaining.html";.