You should find the canopy on the '109 fairly straight forward Arlo, as it's all 'square' angles. Just take your time, place the tape, and cut out the areas for each frame using a new, sharp blade. Make sure you press the tape tight into any recessed framework, and run a finger nail, or the back of your scalpel blade along the line, to ensure it's stuck down firmly. If you lightly rub a pencil along the engraved (or raised) framework, it'll show up, making it easier to follow the line.
I also normally use a paintbrush for canopies, unless they're part of the structure, for example on a B26. I normally paint the internal colour of the frame first, even if this has already been done inside the canopy. It not only gives more 'backing' to the internal colour, but also provides a 'key' for the first coat of the desired externall colour. Two coats should be sufficient for the colour scheme of a Bf109 Trop, depending if thinned or not, but don't try to do it with one thick coat! As with all painting, two or more thin coats are always better than one, thick, lumpy coat!!