Is there a way to keep theme settings when it's deactivated?

I have a plugin called virtual theme which lets you have different address bar paths to look at selected themes. But when you set it up, and make it point to a different theme for each path, it doesn’t keep the settings you make when you have the theme activated on the main domain.

For example, the main theme would be seen here: http://siteproofing.co.cc

but the virtual theme themes would be here: http://siteproofing.co.cc/1, http://siteproofing.co.cc/2, http://siteproofing.co.cc/3, http://siteproofing.co.cc/4, etc. different themes on each address.

But they don’t use the default settings and you can’t change them I don’t think. So is there a way to have the settings made for each theme for the virtual theme plugin?

Maybe make the settings in the actual theme folder in the FTP area?

Please help. Thanks