If you think that the finish on the paint is smooth and shiny enough put the decals on. Xtracryix are normally OK to decal, how ever, some will give a gloss coat before the decals. Its a better safe than sorry situation. You might risk silvering in the decals. This is caused by microscopic air bubbles in the surface of the paint, hence the clear parts of the decal appear silver. By having a shiny surface, the risk of this is significantly reduced.
The matt varnish is the very last thing to go on. That will mean AFTER the decals (and if you dare yet, weathering).
The canopy. Dip it in Klear then stand it on a bit of kitchen paper, to soak away any excess. Some times the clear can pool in the corners of frames. this can be removed simply with a dry brush. Just touch the tip to in and it will wick it away. Put a plastic cup or glass over it while it dries, to keep the dust of until it is dry. Klear is a dust magnet.
There are many different ways to mask a canopy. none are wrong none are the right way. Its a case of finding the one that works for you. I would suggest painting the outside.
You can cut thin, 1-2mm strips and place this on the window part tight to the frame, then fill the rest with more cut to size tape. You can also, particularly on flat square canopies such as the one you have, place a tape over the whole part. Burnish the tape into the edges with a cocktail stick. Then after a cup of tea, or a cigarette, what ever calms your hand. its a new blade in the scalpel and go for it. A fine point and new blade requires very little pressure to cut the tape and by following the frames, you can cut in the corner. Mistakes happen and we all have buggered a canopy or two.
Hope you are not scared off.
Ian M