I apologize for not using the hand convertor. My hand history is not saved. This text is copied from pt.

MP+1: 110.82 BB
CO: 95.96 BB (8$ bounty)
Hero (SB): 93.73 BB (7,50$ bounty)
BB: 22.22 BB (3$ bounty)

8 players post ante of 0.13 BB, Hero posts SB 0.5 BB, BB posts BB 1 BB

Pre Flop: (pot: 2.5 BB) Hero has 9d 9c
fold, fold, fold, MP+1 raises to 2.2 BB, CO calls 2.2 BB, fold, Hero calls 1.7 BB, BB raises to 9.29 BB, MP+1 calls 7.09 BB, CO calls 7.09 BB, Hero raises to 93.61 BB and is all-in, BB calls 12.81 BB and is all-in, fold, CO calls 84.32 BB

Flop : (219.61 BB, 3 players) 6d Jh 3h

Turn : (219.61 BB, 3 players) Td

River : (219.61 BB, 3 players) 8h

CO shows Ad Jd (One Pair, Jacks)
Main Pot [76.58 BB]: (Pre 23%, Flop 77%, Turn 81%)
Side Pot [143.03 BB]: (Pre 42%, Flop 91%, Turn 95%)

Hero shows 9d 9c (One Pair, Nines)
Main Pot [76.58 BB]: (Pre 45%, Flop 9%, Turn 5%)
Side Pot [143.03 BB]: (Pre 58%, Flop 9%, Turn 5%)

BB shows As Kd (High Card, Ace)
Main Pot [76.58 BB]: (Pre 33%, Flop 14%, Turn 14%)

CO wins 219.61 BB

I feel like I made mistake when I did not 3-Bet. In that case, after BB jams, I think CO is folding, or even if he calls the BB shove, now my 5-Bet all-in is much stronger and he is most likely folding? The reason I did not 3-Bet: both players before me have very little % folding to 3-Bet and I am out of position and there are many flops I would not like to play. So my plan was either hit the set or low board or, I hoped that BB after me would shove.
He decides to 3-Bet and gets called twice. Should I ever be going all-in with 99 and Ais it too obvious that my range is 55-TT? I sometimes balance some KK+ hands when I feel like there could be a jam after my call when many players call pf. What do you think is the right play? Did the CO villain make the right call, considering that there was much bounty as well?

You're right that it's a 3-bet the first time action gets to you. I would normally 3-bet pre-flop against a single raise but we should be even more inclined to here when there's dead money from a caller as well and we'll be out of position post.

As played, I really like your shove when action gets back to you. There's a ton of money in the pot; you have good fold equity; and you're very live when called. Nice jam there!

When the first time action gets to you: I tend to flat a lot in these spots on PKO tournaments; we want to get BB to join the action and if we 3bet there is a bigger chance he will fold. It might be a leak in my game.

When action gets back to you: I think I agree with the 3bet due to the amount of dead money. CO can be calling very wide here because of BB's bounty so we have some fold equity and there is a good chance that we are still ahead.

Im going to disagree with Collin Moshman here which means I am probably wrong, lol, but wanted to give my opinion on the hand. I don't like 3 betting pre on either occasion we have the chance to. In a normal tournament I get 3 betting the first time around as long as you are going against opponents you think will fold. Also, your 3 bet would have to bigger than you think for that to happen. Now put us in a bounty tournament where the raiser and the caller have us covered and we have a decent bounty on our head and I just think we are not getting enough folds here to put in a raise. Also considering what I just mentioned we are not getting away with raising to 12BB here and getting folds, we would really have to go large and if we get called, a big chunk of our stack is in and we would be out of position. We would have to play the hand being non flop dependent and basically firing away no matter what comes down. I really dont like playing like that. I want the BB in this hand since that is the only bounty I can win so I like set mining here and just calling first time around and also second time around. Both villains will call us light if we raise and by light I dont mean A8 and A7 which I would want to have call but I mean A10 and broadway hands that are flipping with us. I dont want to be flipping with this size stack. Just call here, hope big blind is in the hand and go from there. Even if we lose the total 9.3 BB we still have a very good stack where bounties can be had later on. I know that is a passive way of playing but imo you have to invite players in the pot that you can win their bounties and also know others will be calling you more than you think to win your bounty.

I think, Hero can both call or 3-bet, when the action first gets to him, but I mostly lean towards 3-betting. A bounty is not a good reason to let BB see a cheap flop. Just because he sees a flop, does not mean, he will stack off postflop, and if he folds, his bounty will not come into play. What will happen much more often is, BB has a hand like KTo and outflops us, because we let him realise his equity cheaply.

And as for the other two guys, we are very deep against them, so our bounty should also not matter much for, how often they call our 3-bet. Individual reads for instance from HUD-stats are more important here than the bounties. Of course I would rather 3-bet 99 against someone, who is willing to fold.

As played I like Heros jam, when the action got back to him. BBs 3-bet size is pretty ridiculous, because it commits him, and I really dont see any reason to play 99 4-way out of position in a spot, where one player is already essentially committed. We either have to fold or jam here, and I think, 99 is strong enough for jamming. If we lose to BB, we still have lots of chips left, so its not a disaster, and the other two guys have very capped ranges, when they just flat his 3-bet.

I expect the two deep stacked players to do a lot of folding, when we jam, and when we get action, I expect to almost never be against TT+ in the side pot. Sometimes we will be against two overcards, as was the case, but this was still a decent spot for Hero with 45% equity in the main pot, 58% in the side pot and some dead chips in the pot as well. Normally 99 is not a stack off preflop for 94BB, but when the opponents have essentially told us, they never have TT+, then 99 is the effective nuts, and I would rather get it in than play some awkward multiway pot out of position.