Hi MrDave and welcome!
You didn't mention whether or not you have and airbrush, but since you're using Alclad I'll assume that you do.
You should spray a light coat or two of the gloss after decaling if the decals are thick to help blend them into the rest of the surface, and/or if you plan to weather the aircraft with washes or other techniques that would degrade the decals. Be sure to wipe away any residue from the decals and setting solutions from the surface before applying any additional clear coats.
I leave the canopy masking on until all painting and clear coating is finished.
There are a number of good flat and light sheen finishes on the market. I happen to like Alclad's Klear Kotes, and have also used Testor's Dullcoat rattle cans with good results. Others will weigh in with their favorites.
Hope this will help you!
Mike