I definatly would not put her in the same place that she spends most of her time durring the day when you are not home. You only have a few hour a day with her and she may start to feel unwanted or left out. Most pets love to be around their family members as much as possible.
I would suggest training her to be in a cage in your room at night to eliminate accidents and having to get up with her during the night. You can also start taking her food and water up after a certion time each night. That really helps take care of night time trips out doors.
Here is my site with some tips on cage and other training that may be helpful:
Training Tips - Dawn's Yorkies Ohio