I think the first question that needs to be asked is:
which two pair have you flopped? Bottom two pair? Top two? One in your hand and one on the board? Aces up, or nines up? Is your second pair vulnerable to counterfeiting?
If your read is you're up against a single player with a straight or flush draw (and nothing else), you should be taking the hand down 65-70% of the time. The OP has actually identified the
least of your problems.
The bigger problem with two-pair type
hands is implied in the questions above: depending on which ones you're holding, you're vulnerable to your bottom pair being counterfeited, your top pair on the flop being bettered on a later street, or being dominated by a set from the beginning.
Your redraws also aren't as good as they would be if you were holding a set on the flop either: without the board doing something runner-runner, you've only got four outs to a full house (as opposed to 10 outs to a boat / quads for the turn and river combined if you're holding a set).