Welcome to YT!
Congratulations, also, on your new little bundle of joy. I have yet had one that didn't cry. Yorkies, you will learn, want to be with you all of the time. They will follow you everywhere and if they can't, they will indeed cry. That's been my experience.
I leave pads down for my yorkie to use if no one is home or if no one can go to the door when she rings the bell to go out. I don't really train to use pads only, so I won't be much help there. I have pads in the garage for night and bad weather. With both of my yorkies, I have found that neither of them would deposit their poopies in the same place they pee. I don't know why, except they are neat, clean little doggies. In the garage, my little Muffin had one designated area with pads where she would poopie and another little designated area with pads where she would pee. The same thing has happened with Kacee. Your little one may well learn in time to go there. I know others do. I just wanted to welcome you and congratulate you on your little puppy and wish you lots of luck. They are precious, but I'll tell you right now that many people find them difficult to housebreak. I've been lucky with Kacee. She was relatively easy and easier than Muffin, in fact. They are all different. Just as people are all different.