He authorized them and got regular updates on the progress in making them. So he definitely knew about them.

He did not live long enough to have concrete plans for them, but he did once ask about using them on Germany (they weren't ready), and when he met with Churchill in September 1944 they agreed that "when a 'bomb' is finally available, it might perhaps, after mature consideration, be used against the Japanese, who should be warned that this bombardment will be repeated until they surrender". That's as much evidence as we have on Roosevelt's own thinking about using the bombs.