never attempt to breed a sick fish, it may be that he is just exhausted but if there is something you don't want to take the chance. i'd regroup and watch them both for a week and then if everything seems good, try again. like sorrell says, the tank is probably too big. bettas can breed in a bucket if you give them a chance (just an example, not a recommendation). water level, no more than 6 inches, lately we have gone even lower at 4 inches. good luck though 

Even if you decide to pull him, there's no way in heck those fry would make it back up top on their own
I still say 6 inches max, my last was in 3