My baby is only 12 weeks old and he is already rolling onto him belly and sleeping. Is it okay to leave him like this?

Always start on back. Do what you can to position babe at the start of the evening. If repositioning from the belly in the night would wake the child avoid it. At 12 wks he should be simply dressed, on a firm mattress with nothing else in the crib/basinette. If the babe is awake when you check in the night reposition on the back until 5-6m. At that point I find it a lost cause.
Rolling over. If rolling over back and front at will then is better not to limit this function by bundling the infant. Make sure the crib is safe (rails long enough to avoid climbing over, rail spaces are narrow enough to avoid head getting stuck or strangulation, no loose cords- strings, or plastics. Wait until baby begins to walk, that will be fun.