Tim,
I use water slide decals and usually paint over them with a catalyzed polyurethane. You can use clear butyrate but you have to be careful to go easy and lay on the clear in thin coats that is not overly thinned or you can melt the decal (or canopy). I usually shoot topcoat over the canopy. Makes it easier to blend the edges of the paint. So yes, you can put a decal on the canopy (or, I suppose, you could put it on the inside and shoot some clear on the inside over it to lock it down) they shoot clear over the top of it.