I recently did this as well, but I started in the middle of one of the sides by feeding both ends of the tube webbing through until half was coming from the two center grommets, essentially locating the midpoint of the line and beginning from there.
I started by lacing the rear half to the midpoint of the other side, then laced the front half to the other midpoint.
This seemed to make it a lot easier to take up the slack when tightening the webbing after the first 'loose lacing', which I did twice to ensure it was tight.
Rocket boxes were almost the perfect height to support the floor while lacing. And I agree the floor goes above the flange attached to the boat. Lacing is easier upside down, so the floor goes under the boat flange.
Hope that helps.