You have to remember she is a little baby...she doesn't know much yet. You will have to teach her EVERYTHING.
Potty training a Yorkie is...a challenge.
After reading many post here on YT about how hard they are to potty training, I knew my little guy would
probably not be fully potty trained until 1 year. He is 9 months old now and is doing really good. He still does not have full run of the house, but we are working on it, one small area at a time.
I believe you should not give your puppy run of the house until she is fully potty trained. You need to give her small amounts of freedom..once she has proven that she can handle it. You can add more room. My little guy, has full run of the downstairs. We are now working on the upstairs rooms. We did have a huge set back when he hit 5 months up until he was neutered at almost 7 months.
As far as your little one not listening. You will need to teacher her what your words mean. You will need to teach her one word at a time. Don't forget to give her a treat when she does a good job! I started with sit, lay, no, come.