Hi Kerri and welcome to YT!! Congratulations on the upcomg litter.
You have come to a great site for help for your mommy.
I am not a breeder but I am a Yorkie Fancier and I own four. I am very interested in breeding so i have been doing some research. I certainly do not know nearly as much as those who have actually whleped even one litter but I might be able to help by pointing you to some good info here and on the web.
This is a link to a site about dystocia (difficulties in delivery) and how to minimize the risk for your little girl starting now. As you are proabably aware small breed dogs have a higher than avberage risk for problems that other breeds so it is always best to be prepared.
http://www.intl.elsevierhealth.com/e-books/pdf/974.pdf
As to your question about separating your female from your other dog there is a thread that was just started recently addressing this very question. Here is the link:
http://www.yorkietalk.com/forums/showthread.php?t=28254
Good luck and please don't be afraid to ask any question on here as the member shere have a wealth of knowledge and info that you won't find in books.
Do you have a mentor? An experienced yorkie breeder who is going to help you whelp this first time ?
Let me know if you don't and I can help you find someone if you like.