I strongly recommend working on the timing of potty breaks. Think scientifically about when he is most likely going to need to go outside, and take him out then. Throw him a party when he does business outside. You will need to accompany him outside; that way he knows when he's done right. I have never had luck with potty pads and puppies; I think it's a bit confusing to them especially if the pad is too close to their 'den'. I do use them with seniors and tinies but they are always right next to the door to encourage the idea that potty belongs outside.
He may also be having his attachment to you reinforced, unintentionally. If you are responding to undesired behavior like crying by providing a positive stimulus like comfort, he is learning that crying works to get what he wants. I would try putting him in his own area while you are home for about 5 minutes and then reward when he is NOT crying...by letting him back to be with you, or giving some other reward. If he is only ever in his special area when alone, he will naturally be upset about it as he associates it with being alone, so he needs to learn it's okay to be there. You can feed him there, give him treats there, until he realizes that it isn't only a place he goes when alone, and it isn't a bad thing. I think right now you may be setting him up for developing anxiety issues.
There are a lot of great resources out there on training dogs, and I don't have one in particular that I recommend, but if your training resource recommends punishing your dog, then it's one to steer clear of. Clearly your pup has a sensitive nature and few dogs respond well to punishments. Yelling, hitting or smacking a puppy or dog is not an acceptable training method (and I'm not suggesting that you're doing that, just saying that if a training 'resource' recommends it, then that's not a resource to use). You want to use a dog's natural instincts of association to build positive associations with desired behaviors.
I would recommend looking into puppy obedience classes as well at a local training establishment. Often, these are run by well-educated dog trainers who not only can help teach beginning manners for your puppy but also assist with things like housebreaking and teaching puppy about being alone. I am a bit wary of the classes run by the big-box pet stores as the quality of trainers there can vary greatly. Some of them are excellent trainers, but some of them have the minimum background in the field and may not be very helpful for you. At best a trainer can help you learn how to teach a dog to be a great companion. At worst they can help you ruin your dog. Caveat emptor.
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