[LunarBerry]

I hear ya, my girl did beautifully the first week or so but after than she started going in the house/off pads. If the weather isn't to her liking she'll just run straight back into the house to do her business. She has designated spots most of the time, doesn't matter if we use those scent removers or ones that help repel them and if we put pads down there hse'll go on the edge >_<. I think in a lot of cases they don't pay attention to the smell/repel so much as they only do their business in a short few seconds lol that and I think she just holds her breath as she goes lol
But yea, yorkies are notorious for being a little bit harder to potty train. It took our past two yorkies about 1-2 years for them to be fully trained. Right now my girl is more harder, as she's been extra spoiled and I find aside from rain, she really doesn't like going outside when it's hot (and it's very hot here in GA) but I don't blame her. I don't believe the sleeping arrangements has anything to do with it so much as she's got more space to go to do her business.
When they are pups they instinctively not do their business on or to close to where they sleep. They learn this from mommy keeping the area clean.
Since it's a new home, she's needing to learn that the inside of the house in general isn't for potty. To her, it's all open space and her den area may be designated by the bedroom. So everything away or outside that room could be considered "outdoors" to her right now.
But she's young and is still learning to control holding it in, so she'll have to be taken out to pee/etc. frequently. Even if it takes her a little bit, once she does, praise/treat her each time. Consistency is the key. You might also start training her to use a bell to let you know when she needs to go.