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""What should I do when I know I'm favorite against my opponent's range and I know a way to get it all in?"

Do it."

But my point is that I don't necessarily want to go up against him since he might have 2 overs and flush draw and therefore be a slight favorite. So pushing to take it right there is better, yes??

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No. This is VERY faulty logic. If his hand range is as wide as you say it is, and he really will get it all in with you with that entire range (This probably isn't actually true; I'm answering the question that you asked.) then you should do it. The fact that that range includes some hands against which this play is incorrect doesn't matter.

For example, suppose you have AK in the SB with blinds at 500/1000. Your opponent in the BB has 1k chips. Do you a) fold because your opponent could have AA, in which case calling would be wrong, or b) get it all in because you have your opponent's range crushed?

I hope this clarifies things.