MP Villain ($224) raises to $4
CO Villain ($98) reraises to $13
SB calls $13
Hero ($333) calls $13 with Q[d]Q[c]
MP Villain calls

Flop ($52)
J[c]3[s]Q[s]
BB checks

Who checks who bets? Both players acting behind me are aggressive.

Normally I would do that too, the reason I'd do it differently here is that the players are aggressive. That means that IF they have the flush draw, they WILL bet it.

well were talking about a raise and a re-raise from a short stack (shorty isn't folding)

I lead out for 3/4 pot, hope MP smooth calls and when shorty shoves all in then and ONLY THEN do I think you have a decision to make that is tough

Then do you re-raise all in to isolate or smooth call hoping MP comes along

up to that point I think this hand plays itself. I really dislike the check raise.

also I know stoney plays a much different style than I do so I don't hate the check raise if I am viewed as "tight" but since I play fairly loose I lead (because I lead with all kinds of crap)

you lead out a bet here, and get it all in fast