Starting backcourt will be Fultz and Thomas.
Thomas will defend opposing point guards and thus be listed as the pg, but Fultz will run more of the offense.
I could also easily see a similar scenario to the one JPotter outlines above. I'd be shocked to see Thomas traded. I expect him to be resigned but wouldn't be surprised to see us let him walk in FA.
It's really hard for me to see a Fultz and IT backcourt working together. Offensively, it could probably work out decently. However, I think people are exaggerating how effective IT is off the ball. Yes, he can play off the ball, but he's much better being the primary ball-handler, playmaker, and scorer, which is why he thrived so well here. He really only played off the ball with Smart because Smart is simply atrocious off the ball as a spot up shooter. I think it's yet to be determined how well Fultz will play off the ball in the NBA.
Defensively, it will clearly be a disaster. Fultz has excellent tools to become a superb defensive player in the future. However, it's going to take him awhile to get there and get used to the NBA defensive game, especially with an increased offensive role that he'll have. As bad as Brown was defensively starting off the beginning of this season, I expect Fultz to be even worse. Hopefully he improves defensively as much as Brown did this season, though.