Ron, For the latest yak we're building we elected to glass the deck after building the cross strips. We found that it made for a stronger deck. We then built the coaming up using a terrific idea of my wife. We then lay wetted out roving in the 90 degree angle and lay 4 oz triaxial glass strips. We're now laminating incredibly resistant maple stips to build the lip. That said...

No, hold off the fill coats till you finished the cockpit. You'll have spills dribbles, drips and all that. Sand and feather everything, wash the deck down with hot water and a green nylon scrub pad because there's always amines in the cured epoxy (hey, I've been learning all about hardeners and ammonia complexes are in 'em all), then a wipedown with denatured alcohol (thanks everyone for that tip), then just because I'm a paranoid, one more wipedown, then do the fill coats taking great care to avoid any contamination.

my two cents worth