I floated the flop because he's an uber donk and I knew that I could get implieed odds.

I CR the turn to see if anyone has the flush, when second villian cold-calls, I'm getting ready to shut down if he shows aggression on the river.

Then the 2nd worst river card comes (if it were a club, that'd be worse) and I have to fold.

PokerStars No-Limit Hold'em, $1.00 BB (5 handed) from (Format: Bet The Pot)

Button ($212.20)
SB ($241)
Hero ($148.75)
UTG ($49.75)
MP ($19.75)

Preflop: Hero is BB with , .
UTG calls $1, 1 fold, Button calls $1, 1 fold, Hero checks.

Flop: ($3.50) , , (3 players)
Hero checks, UTG checks, Button bets $3, Hero calls $3, UTG calls $3.

Turn: ($12.50) (3 players)
Hero checks, UTG checks, Button bets $6, Hero raises to $18, UTG calls $18, Button calls $12.

River: ($66.50) (3 players)
Hero checks, UTG checks, Button bets $27, Hero folds, UTG calls $27.

Final Pot: $120.50

Results in white below:
UTG has 6s 6h (three of a kind, sixes).
Button has 9c Qc (flush, ace high).
Outcome: Button wins $120.50.

Putting in a lot of money to find out where you stand is hardly ever a good idea.

What's the alternate line...check-calling? Leading...what if raised? Etc...

Not a lot of money went in on the CR. I suppose the alternative is to check-call down as it'd likely be about the same amount as the CR (slightly more, I'd imagine). It wasn't JUST to find out where I was - if I was ahead, then I wanted to charge more for the FD.