Hi Jennifer,
To answer your questions...
Do you still have his potty location inside the large crate or did you switch the location once he learned to go on the pads? I actually disassembled the crate. When I'm at home, he pretty much as free run of the house. I used to watch his every move. He likes to be in the same room as me for the most part, so its not difficult to keep an eye on him. When I'm at work or school I have him confined in the kitchen with a baby gate. I know you described that your apartment would be difficult to do this with, so the crate might be a good idea for you.
If so, does Stewie know to go into the crate's open door to use the pee pad when you're home and he's free in the house? I have a pee pad in the kitchen (downstairs) and one in the corner of my bedroom (upstairs) where he spends most of his time. When he has to go, he just jumps down off the couch or bed or wherever and goes, then runs back looking for a treat.
What do you do at night? We share a pillow.

He's in bed with me most of the time; sometimes he hops out to munch on some food or lay on top of the heating vent. 90% of the time he is in bed. Sometimes on weekends if I am sleeping in, he will get up at 7AM or so to pee and then crawls back in 'til I get up.
Many people on this forum use only positive reinforcement to train their dogs to be housebroken... like ignoring it when they have an accident. It definitely didn't work for me.
Here's what I did:
When I caught Stewie in the act of peeing anywhere but his pad, I would say "No, that is not where you go potty" in a stern voice and pick him up and put him on his pad. Then, I would use a happy voice and keep repeating "make potty".
After that, if I saw him sniffing around on the carpet, I would say "make potty on your pad stewie" over and over in a happy voice. He eventually caught on and would go seek out the pad. Sometimes, randomly, I would just put him on there and make him stay on there for a few minutes while I repeated "make potty on your pad". I know I must've looked and sounded crazy.
Now that he's potty trained I am soooo happy! It just takes a lot of time. I was a miserable Yorkie Mommy the first few weeks, but now he is just great company since I don't have to worry about him messing up my house with pee and poo.
Anyway, good luck with your pooch. I hope I helped you a little!
EDIT: Forgot to mention that when he got it right and went on his pad, I would literally freak out and go crazy for him so he knew he did a good job. I would also give him a small treat. I am still giving him treats, but I am making them smaller and smaller. He's so funny; sometimes he pees like not even the size of a dime just so he can get a treat