Before you attempt to touch it up, try a scratch remover. I recommend Meguiars Scratch X. It comes in a black tube. I detail cars, and this is by far the best scratch remover out there on the market. Clean the area, then apply the product with a soft terry cloth in a circular motion. Let haze, then buff off. This one will get out some white scratches too, so its worth a shot from what you are telling me.
If this doesn't work, then 1) Bring it to a body shop, they can buff it out with a machine. 2) Then, try touching it up yourself using touch up paint that you bought.
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2000 Hyundai Elantra GLS (Photochop)
-PIAA 1100 series driving lights
-PIAA Plasma Headlights
-10" Pioneer sub powered by Kenwood 600 watt amp