A little more patience, she's only 13 weeks old. Many yorkies won't poo and pee in the same spot, try getting her on a routine and learn when she needs to poo and make sure she goes outside or to the pad when you think it's time for her to poo. Rizzo could never learn to poo on the pad either, but he has to make poo twice a day, once in the am and once in the evening, I just make sure to have him outside when he needs to, or I'm cleaning the floors for my mistake.
Good luck, you are off to a great start if she is going on the pads most of the time
