Canopies are probably the only thing that I don't prime, due to the fact that the first color you put on the canopy is going to be visible from some angle. Using the F-16 I'm building as an example, I started off by masking the front and rear canopies inside and outside for my first color, which is Tamiya X-18 semi-gloss black. The inside of the real-world F-16 is black, and then the outside has kind of a rubber seal around the perimeter which is also black. Once that was done, I left the masking on the inside (a combination of Tamiya vinyl tape on the edges of the frame, and liquid mask to cover the rest) to make absolutely sure that nothing gets on the clear part during the rest of the process. On the outside, I removed the first mask for the "rubber" color (the Eduard mask kit has masks for the two color layers). Then I applied the second mask for the fuselage color, using the liquid mask again to fill the areas not covered by the Eduard mask, per their instructions. Once the outside of the two canopy pieces were remasked, I used tiny snakes of Blue Tack along the edges (including the mating edges of the canopy pieces) to both temporarily attach the canopy to the model and protect the detail work in the cockpit from any overspray which might sneak in under/around the canopy. After that I started with decanted Tamiya grey primer for the whole model, checked/corrected any remaining microscopic seams and gaps, painted, gloss clear coated, decaled, weathered with Flory wash, and then flat clear coated. After all of that was done, then I finally removed the canopy pieces, the masking, and then dabbed up the left-over chunks of Blue Tack. I'm waiting to permanently attach the rear canopy piece until after all of the work on the bottom of the plane is done, just so I don't risk scratching or cracking it while the plane is on its back. When I attach it permanently, I'll be using Devcon clear epoxy. The forward canopy I'll be attaching to its rail the same way, once I attach my scratchbuilt JHMCS sensor (haven't made it yet...so hoping for the best) and get the assembly painted black.
WHEW!!! As you can see, canopies can be quite a process, and they're definitely not an area to try to rush since they're the window to all that nice cockpit and interior work that you've already done.
Here it is, all masked up.
And here it is, the finished canopy just sitting on the model after unmasking.