Masking canopies is tough. There are usually several panes and complex curves to deal with, plus the lines have to be straight and you have to be careful not to scratch the clear plastic.
There have been several posts here about it so you'll probably get several answers. This is just how I do it.
The first thing I do is mask the INSIDE of the canopy. I do this for two reasons: 1) So I don't forget it (I did that once and ruined a canopy) and 2) Because my hands are always very dry and dry skin can leave scratches on the plastic!
Next comes the outside. I use Tamiya masking tape because it is thin enough for me to see the panel lines underneath. Stick a piece on the canopy, and use your finger nail to push it down VERY WELL along the panel lines. The better it is stuck, the better you can see the panel lines, and the easier it is to cut. Then use a very sharp X-Acto knife blade to trim the tape. Make sure the knife blade is very sharp so you get the tape cut cleanly. Take your time! Work slowly and get the cuts nice and straight.
The trick is to make sure you know where the panel line is, and cut right against it. If you mess up a cut, don't try to salvage it. Rip the piece of tape off, put a new one on, and start over.