Congratulations on rescuing a dog and changing the rest of her life.
The reason she goes inside and doesn't let you know is most likely that she was never taught otherwise. Whether she was confined to a crate for hours on end or what, she wasn't taught potty manners. One idea that might help (not sure) is when you clean up her pee and poop bring it outside so the scent is there. Then when you take her outside she'll smell it and know that is the potty area.
It's great that she's trusting enough to let you carry her. You may want to encourage her to walk on a leash next to you by hooking the leash to your belt buckle so she can be with you all the time if that's what she likes (which will also help with potty training).
Good luck and yay for you for rescuing a yorkie
Lots of people on here will be able to give you help!