On the Styles / Files tab, where you set the "custom.css" added to your styles list, there's also a box there for adding custom _theme_ files. So typically I'd add something like customT.Css there. Then in each theme you can have a different cstomT.css file.
So, in other words, you can add custom files that are "common" and in the styles folder, and files which are in the themes\whatever folders, and which are different for each theme.
cheers
Bruce