Discoloration on dogs legs..?

I have a dog that is now 2 years old. And we lived in an area infested with cats and fleas, we moved about a month ago to another flea free home. He is still recovering all the flea bites, he had really bad bites and was really infest with fleas but now his skin looks discolored, like black/burnt color. It is on his back side near the upper thighs and on his private parts. The skin itself is discolored, when I pass my hand to see if it is bruised or if it hurts him but it does not bug him at all. Can anyone suggest what it is and will that discoloration go away with time? I have aloe vera can I keep adding that, if that will help? When he had a lot of them he was soo itchy that he pulled his hairs out just to scratch himself. Now his hairs are growing back nicely. He is always with a happy attitude never sad or sleeping all the time likes to play a lot now that he is in our new place. So if any one can suggest something or what I can put on him to take that discoloration away. I have a benedryl cream, can I put that on him if he needs it too? thanks in advanced. Ohh another note his bowel movements were a little off and now its good, also his eating habits are a little off he doesn't finish all the food on his plate. He usually eats it later in the day..