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Is Puppy Confused?

How do I get my dog to go potty in the crate?

Before trying to answer your questions can you tell me what your long term training goal is?  Also how much time she is spending in her crate?  Are you away from her for extended periods?
He'll have to be in his crate during the school day; although my mom has been "puppy sitting" so he hasn't been alone for more than a few hours. He will urinate in the crate or on a pad in the kitchen for the most part. I bought that the house training aid to spray, but don't think it's working. We put him in a bathroom if he has an accident.  He is much less reliable with pooping. I was wondering about making sure he spends time in his crate right after he eats? I feel like we're starting to veer off course. Thank you.
The time he spends with your mom may be confusing in that he may be too far from pad/ crate when the need arises. He should be in the crate whenever not actively engaged in play.
After play or eating it is best to carry him back to the area where the crate is either in a small play pen or bathroom. Once he spends more time in the crate while you are away it will likely go better.
It sounds like we may be giving him too much freedom? When one if us is home, we let him wander around the house. Is that okay?
For short periods after he eliminates but not before. Going from crate, to crate in small area, to free roam over the first 3 weeks is ideal.