[bodywerks]

To do it right will require paint around the canopy/hatch line at the least. The best way to do it would be to just paint the whole hatch because it will eliminate any mismatches between the covering and paint and would match the paint on the cowl exactly. But it can be done with a combination of covering and paint:
Trim the canopy to the point that you are ready to glue it down.
Position it where you want it and secure it with a few pieces of tape.
mark around it with a marker and remove the canopy.
Take some 60-80 grit and sand a groove in the hatch behind the marker line so that the canopy fits nearly flush with the balsa.
Sand the under side of the canopy where it will attach to the hatch and glue it down with some 30+ minute eopxy/milled fiberglass.
Decide where your paint line will be on the canopy and then mask about 1/8" below that.
If there are gaps or voids or high spots around the canopy/hatch joint line, fill them with a high-quality body filler, like corvette repair filler/bondo and then sand a smooth contour.
Once close, paint with a sandable primer. You will find that it is easier to fair it into the hatch by moving the mask line on the wood after each coat. Once dry, sand to a smooth contour that fairs into the wood and the canopy seamlessly.
Now paint the area of the canopy line that you are sure you will not be able to make it to with the covering. You'll want to blend this seamlessly into the hatch as well or it will show up under the covering.
Now take some 1/8" fineline tape and make a mask line up to where you think you can apply covering and leave it there and start applying the covering. The masking tape will show up as an impression under the covering to tell you that you have applied it far enough up. Once the covering is applied, use a fresh #11 blade to trace around the mask line and remove the excess covering and masking tape.
I might have a few pics at home of the canopy install I did on a 34% CHP that I will post when I get home.