I have a 2 year old pure bred German Shepherd named Dante.
I trained him myself and up until he was about 2 months old he had grasped the concept of house training very well, being a German Shepherd he is quite intelligent.
I had got him in the beginning of July and was home with him 24/7 until I started school in the September (my grade 12 year) he was 2 months old and started to protest because I wasn't with him all the time. I corrected the problem and he stopped. We got another dog, an older dog for him to play with and learn from when he was almost a year old, he didn't protest or seem to have a problem with him (his name is Atticus, he's a German ShepherdxCollie, and about 5 years old) they get along great together. But recently, within the past couple months he keeps peeing on the floor! I know it is Dante because he isn't fixed, so he cocks his leg, I've witnessed Atticus going to the bathroom and he squats (which is kind of weird for a male, but he's fixed). The urine is in 2 places, against a kitchen chair that is in our dining room and against our two couches. We have cleaned the area with bleach, with vingear(it's supposed to get rid of the smell so they don't continue to do it), we've moved the furniture, we can't think of anything else to do. It's driving us nuts because the whole house smells like urine all the time. I've taken him to the vet, there is nothing wrong with him, he is perfectly healthy there is no medical reason for it and on top of it all he'll wake me or my mother up to go outside several times through out the night and do his business and stay out there for hours at a time. It is driving me up the wall because yelling at him does nothing, it scares him and he ends up peeing in fear. I know he understands, he is very intelligent, extremely intelligent, I don't understand why he's doing it. Is there anything else I can do, or do I just need to continue to clean the area like crazy?

Don't yell at him. There's a great book out there called how to housebreak your dog in 7 days. It's short, sweet and to the point. It's also cheap. If you can't get it at your local bookstore, you can definitely find it on amazon.com. Other dog training books should also have a section in it that should help you.

I think you should consider house training your dog from square one to instill the good habits and break the old ones. If he's always peeing in the same places, you can divide his meals into various plates and put them where he's been peeing. Keep one in his usual place. Keep this up for a few weeks. As they say, a dog never pees where he eats... and vice versa.