I noticed something scratched an area between the the driver and passenger door of my car. It is on the black strip on the drivers door, along the edge. I can see gray, im not sure if this is the primer or not. Does anyone know what i can use to fix or touch this up? Should I bring it to a bodyshop or dealer to fix it?

Here is a pic, i dont have a pic of my car yet, but here is another P5 that I am using for illustration.

 

The dealer should be able to get you a bottle of touch-up paint. If not I know Ford sells black accent paint through it's dealers.
I'm not sure if the Protege is painted there or not but at Honda (my company I work for supplies to Honda and Toyota)they apply a black tape to those areas sort of like a decal.
If all else fails consider having a body shop blow it in, maybe in a colour matching yours...could look cool! Good things can always come from the bad!

 

Go to the dealer and look at other P5s in the lot to compare. If you determine it is a factory defect, the dealer has to fix it free of charge.