Pot Odds vs. Implied Odds

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I posted this in the Beginner's forum, but would also like to help from this group.
Confused on how to use odds. Let's say I flopped the nut flush draw, giving me 9 outs and 4:1 odds against. My opponent has $12 stack and I have him covered. He bets $2 into a $2 pot. Do I use the pot odds $4 pot, $2 to call, 2:1 or do I use $4 pot plus $10 stack behind, 7:1 to make my decision?
What I have been doing is looking at how much my opponent has already committed to the pot. If he has committed less than 1/3 third of his stack, I'll look at the present pot odds. If he has already committed more than 1/3 of his stack, I'll look at his stack size, figuring he is likely to play for the entire stack. Does this logic make sense?