|The first problem you have is that he was left in his crate too long without being able to relieve himself. A young puppy can't hold it for that long any more than a human infant can. Dogs don't want to go where they sleep, which is why crate training can be so effective, 'cause they'll hold it as long as they can. However, once a dog has become accustomed to having to eliminate in their crates, it's nearly impossible to break them of it.
My advice is to block off a portion of the house, I used my bathroom since it had a tile floor and I could close the door. Put the crate in that room, after cleaning it thoroughly with bleach, rinsing it well and letting it air dry. Don't use ammonia, that smells like pee to them, the whole point is to remove all possible traces of pee pee odor.
Also put the litter tray in the room. I use clumping cat litter, since the Second Nature is so large that it must be like walking on small logs for little chihuahua feet. I did a lot better with training once I switched.
Put puppy into the room and into his crate, but do not close the door to the crate. Make sure he has a soft pad to sleep on and a blankie to snuggle under. Also make sure he has at least one safe toy to play with. That way, he can sleep in his cozy crate, but will be able to leave it to eliminate. If he makes a mess with the litter, just sweep it up and put it back in the tray. This goes for when you're both away at work and at night when you are both sleeping.
Puppy should from now on use the tray. When you get home or get up in the morning, go into the bathroom and stay with him until he goes, that way you can make sure he goes in the tray, and then make a big deal about how he's a good dog to go potty in the litter tray. I actually use the words "Good girl/boy go potty in the litter tray".
I would suggest feeding him in that room too, since after he eats or drinks he'll have to go potty again, and the tray will be right there. Again, you have a chance to observe, guide and praise.
What you mustn't do is use the room for is punishment. Unless you catch him in the act, yelling won't help, 'cause he won't connect pee on the floor with an angry human. All he'll know is that all of the sudden you went nuts and started yelling. If you find he's gone somewhere other than the litter tray, or if he has an accident while you're home and he's out with you, just calmly clean it up and use a deodorizer specially formulated for pets, Febreeze won't work.
Until he gets to be around six months old, he's not reliable, no puppy of any breed is. It's your responsibility to take him to his tray when he wakes up, after he eats, after he plays, before he goes to sleep, if it's been a couple of hours since the last time you took him, etc. He wants to make you happy, help him figure out how by praising him when he goes where he should. It may also help him to not lift the leg if you have him neutered before he turns six months also.