The canopy must be trimmed to a perfect fit! (Take you time here) Second Hold the airplane so when your gluing with ThinSet CA the glue runs out of instead of into the canopy. (important) After you are satisfied with canopy placement finish gluing. The next thing I do is tape off a line where canopy in real life would meet the fuse. leaving the edge line exposed for scuffing. After scuffing with 80 grit I paint to match fuse. Let paint dry. Lightly sand with 220 and now we are ready for epoxoliting around the canopy. tape a second line while leaving the tape on the canopy around the parameter. About a 1/4 inch will do. Mix Epoxolite and micro balloons at 60% Epoxolite and 40% micro balloons. Now smear it around the perimeter and smooth out. Care should be taken here as the time you spend here will save you time sanding.

After gluing with CA I scuff a 1/4 inch all around the bottom of canopy with 80 grit. Then tape a line to canopy edge and paint to match fuse. Let dry. The I mix Epoxolite with micro balloons about 60ty 40ty Don't mix up more than you can work in about a 5 min span. By adding micro balloons it kicks off faster. Smooth with finger to tape line. If done right you have a painted rim inside and epoxy outside. The most important part here is the smoothing. Epoxolite is hard so care now will save sanding.
The last thing to do before removing the tape is a coat of primer and finish sand. That's the long and short of it. If you follow these steps you will have a canopy that looks like it belongs on the plane. Good luck! Questions just ask.

Here are some links on how to dye canopies From Walter Umland