Repairing a scratch in a car

Hi! I scratched my car (Mercedes, 2006) at the part next to the right rear wheel . At one spot of the scratch the metal can be seen. My car is not new but I like it and I am concerned about it getting rusty due to exposure of the metal. I went to a Mercedes shop and they told me to use a touch-up paint to cover the scratch. I am not sure if this will be enough. Would the touch-up paint provide sufficient protection for a scratch that is down to the metal? Also, I am not experienced in this kind of stuff and I am afraid of making it worse. Is there a place you can recommend where I can have this done at a reasonable price? Any advice will be appreciated.