Since you have a tube, and not the U shaped rails from the factory, I think I would drill a bunch of holes in the floor pan and spotweld to the topside of the rail, and also stitch them on the side on the bottom side of the floor. Use a weld thru primer on the top of the rail and bottom of the floor so you don't end up with rust in that joint, since if water gets in, it's unlikely to get out.
What you could also do, is cut the floor in half longways, and bend the edges 90 degrees to make your flange, and spot/stitch weld as needed. That way you don't end up with the possibility of moisture gathering between the floor and rail.