Iphone and find my iPhone I am wondering if the owner of the phone I am tracking using find my iPhone can see that I am tracking them in real time or any other way.
Any service (Find my Friends, Find my iPhone etc) that requests the location will show the little compass icon in the status bar as the location is requested.

You can also see apps that have recently accessed your location within the last 24 hours in Settings > Privacy > Location Services

For more information, see iOS 6: Understanding Location Services