Cat help?

I'm asking for advice on cat dynamics. I'm gong to explain the cats and the situation involved in detail, and the specific question is below the cut.

Here's the situation. Mike and I have two cats. One is a female, Athena, who is about four years old. We got her from the animal shelter last year. She seems to have been traumatized at some point in her past, probably via whatever landed her in the shelter as a three-year-old spayed cat who had obviously been someone's pet. The shelter found her...