Glass first. I like to cut out a rough opening for the cockpit at least an inch inside the lines and glass to that. I'm usually using shorter strips that end in the cockpit opening anyhow so there's always a bit of a rough cockpit opening.

You don't want to glass a deck right up to a coaming. I'm sure it could be done but it would create a lot of gussets and a lot of problems with air pockets etc.