He does definitely have the alpha position, and he knows it.

Get rid of the puppy pads – they only encourage going in the house.
Get him on a set schedule. It doesn’t matter if he likes it or not, you are the pack leader and he will follow. It may take a little time, but he will listen.
Make sure his crate is large enough for him to stand and lay down comfortably, but no bigger. The more room he has, the more space he has to go potty in. If he goes potty, it will be right in his space, and a couple of times should break him of going inside.
When you take him outside, go to the same area of the yard, and tell him to “go potty”. Once he does, a lot of praise, and the occasional treat.
When you cannot be with him, he’s in his crate.
For training, although many folks believe a treat is the only way to train a dog, this does cause problems once the treat goes away. Teach him his commands without any treats, using you voice, your leash and collar, and if necessary, your hands. Your instructor should also go through proper methods of training.

The hardest thing from what you are saying is that you need to take the lead, and make the dog listen to you. I’m not saying be mean or cruel, but you need to be firm. You are the alpha of the pack, and he needs to understand this.