You should 3ball him preflop. ATs is fairly strong 3 handed.

If you dont 3ball him, the flop checkraise is good. You should really lead the turn though. If he has an ace expect him to raise you. If he was a big donk you could 3ball him there too. The doulbe check-raise is too risky. If he checks it through, you lose a good deal of bets.

Okay, back the the scenario where you do 3ball him preflop. Bet the flop, if he raises you can reraise if you want , but I would probably just call. This is because if he is really aggro you can check-raise the turn here (which you will likely be able to since an ace hits in this case. Either way, I'm leading the river.

The nine pairing isnt really a big deal. Its not likely they have a nine.