Having some problems with Thesis + MU

Hello everyone.

I am working on my first MU project, a blog network for all our real estate agents in our company.

I would like to use Thesis as the base theme. What I am trying to accomplish is being able to use Thesis for all my member blogs, being able to customize each instance of the blog with different background colors, header image and a custom footer.

Using the Thesis open hook plugin, I am able to accomplish most everything I need. The Thesis design options however are controlling ALL the blogs in the network as opposed to the individual installs. So when I switch to a 2 column layout, it changes all the sites using Thesis to a 2 column.

A workaround I thought of is to have two separate theme folders, a 2 column and a 3 column. But there could be other problems down the road that I have not discovered yet of one site's settings trickling into the other sites.

Has anyone here used Thesis as a base them, and if so, what did you do to solve the problem with the options in each blog affecting all the others?

Researching the Thesis forums, still have not found an answer.