Hi Unreal23 and welcome to PT!! As you cn see, I'm in Wylie(just north of Garland). Nice to have a close neighbor aboard!! We just recently adopted Millie and had some separation issues with her as well. As Aly said, probably the best thing to do is the in and out thing. That worked the best for Millie, though it did take some time. As someone who grew up with a chi, don't worry, with time and the right goodies Cookie can learn anything you want to teach her.
As far as discipline, in the beginning with Millie, I didn't raise my voice at her when I reprimanded her. If I did even slightly, she peed. Now (2 months later) I could even yell at her and she'd just stare at me like I'm crazy.
If you don't want her in the bed with you, I'd suggest a crate, too. That way she won't hurt herself or your apt.
We also dropped treats for Millie while my husband and I were getting ready for work in the morning (or anytime we left) to help associate our leaving with something good. We didn't hand them to her, our trainer suggested that they just "fall" from the sky. Worked like a charm.
Good luck with little Cookie.