it takes time and patience. Time and Patience. Time and Patience
Specially if you travel and stuff. If you want to use a littler box, you have to take him there a while after he eats so he can go there. He may not go there for sometime, but an exercise you have to do. You have to keep an eye on him at all time, and if you see that he's trying to go somewhere else taking him fast to the box, even if he has gone in the wrong place already, say no, and take him to the box and say "here". If you can't be paying attention at what he's doing at a given time, put him on a crate, so he won't go anywhere in the house.
Remember, it will take time. And 3 month is very young... usually yorkies take time to train... some may be trained at 5 months, while other may take almost a year.