You want to fill the weave on the outside of the hull as soon as the epoxy is hard to the touch so you get a chemical bond. If it's been a while, you need to scrub the surface with a stiff brush or scotch bright pad to make sure no blush has formed which will compromise your fill coats adhesion. You can use water and some detergent for that. Scrub it good wiping it with paper towels.

When you glass the top deck, don't wait to fill the weave. Also make sure you keep a few stations in the hull to prevent distortion as it cures or spreader bars like you're doing. The order you work is not as important as filling the weave right away in the areas that need to be filled.

I usually do the outside hull and then go on to the deck as the outside glassing is curing good. Because the deck is much flatter, it doesn't want to curl like the deck can. Cut the cockpit opening after all the glassing is done.