He will in due time!
Its going to take some time and you are going to need to get some more patience with him. I know what you mean by ruined carpets, Ive got my fair share, and many people here have replaced their carpets with hardwood or linoleum bc they were ruined from their lovable but chronically peeing pups! I know you researched before you bought your pup and found many many things on little dogs (aka - yorkies) being difficult to potty train right?? 12 weeks = way too early
Hang in there, once he gets it down you will have a perfect companion for life! The first few months of kind of misery (get ready for the chewing stage) will be worth a lifetime of sweet yorkie kisses!