Awww, glad to hear that surgery was going well. LIke I said, 90% of the stress will be alleviated once your surgeon calls and tells you that all is well.
I was told by another YT member who was a tech, to be careful with putting too many blankies and pillows in the crate as she could possibly getting tangled up in them. I would suggest that you put it in a pillow case and sew it up to make a cushion. That is a very good idea to put your scent on it-she will be with mommy.
I know that it will be hard to crate her, but it is for her protection and well being. Be strong, that's the hardest part. There is light at the end of the 6 week tunnel!