The pup is not even 12 weeks old yet, he cant be expected to be house trained.
You probably wont see much progress until the pup is around 4-5 months old, yorkies are small dogs and their bladders are tiny. They cant hold it for long especially at that age.
When training Poppy my BF told me to rub her nose in it. I was horrified and told him if ANYONE was getting their nose rubbed in pee it wouldnt be HER.
So what I did was when I caught her peeing or pooping on the carpet I picked her up took her to the accident and held her close (NOT rubbing her nose in it) with her face a few cm's away so she knew what she was getting wrong for and told her NO then put her straight on the pad/outside.
Seen as your BF is home alone with your pup for 3 hours a day you need to tell him you are totally against him rubbing the pups face in the accident, and maybe suggest what I did and show the pup the accident before putting him on the pad.
Good luck!