ATs with 2nd pair and Nut Flush on Flop

Known Players:
MP2: $3.99 - 200 bb
MP3: $2.08 - 104 bb
CO: $0.72 - 36 bb
BU: $1.95 - 98 bb
SB: $1.84 - 92 bb
BB: $1.77 - 89 bb

0.01/0.02 No Limit Hold'em (6 Handed)
Hand recorder for this hand: PokerStrategy.com SideKick 1.0.50906.2

Preflop: Hero is MP3 with A♥, T♥
SB posts small blind ($0.01), BB posts big blind ($0.02), MP2 raises for $0.06, Hero calls, 4 folds

Flop: ($0.15 - 7.50 bb) Q♥, T♠, 8♥ (2 Players)
MP2 bets $0.11, Hero raises for $0.32, MP2 calls

Turn: ($0.79 - 39.50 bb) T♣ (2 Players)
MP2 checks, Hero checks

River: ($0.79 - 39.50 bb) 9♦ (2 Players)
MP2 checks, Hero ???

[PreFlop]I decided to flat call here with ATs, because there are another two TAGs behinds me and wait for their action. Should a 3bet have been better here?

[Flop] The MP2 Cbet, but with 2nd pair of Tens and nut flush draw, I wanted to put more money in the pot as much as possible, so a Raise should be more reasonable here. Addtionally, I assumed my opponent's range could include JJ+, KQs, AQ, AK or 88 flopped with a set.

[Turn] A trip for me, but could be a fullhouse for my opponent. It's better off checking behind than putting any bet here.

[River] My hand could be beaten by many hands of his range, should I have checked behind to minimize losses or just to put a small bet to make him call with worse hand like KQ, AQ?