It would be a lot easier to fill any gaps now ,than after the door bars are in .For sure!
One method I've used is that after the base plates are welded where its' tight ,use a floor jack with an old socket or something and push the floor up to meet your base plate. Floor pans seem to be the lightest gauge steel in the car. It's worked for me and I prefer to have them welded continuously, just like the bars. Hope this helps.
Chris