Comment 2 for bug 591425

I see now that after customizing a theme to your liking (e.g. size and panel behavior), you can go to the "Themes" tab, then click "customize", export the theme somewhere, then install the theme again. So this does work as a way to preserve one's settings while trying out some other themes, but it is not very user friendly in my opinion and is little help to someone who tries a new theme and finds certain panel settings lost.

I would suggest, if possible, following the example of the "Appearance Preferences" dialog in Gnome (or perhaps it's Ubuntu specific), where any changes made to things set by themes automatically get saved as a Custom theme, which is then automatically overwritten anytime you customize a theme. Another thing from that dialog that would be neat to have is a little popup that occurs when a theme is changing certain attributes (i.e panel size and behavior for AWN, although it triggers for window buttons placement in the Gnome dialog) that says something to the effect of "This theme suggests a panel size and behavior. Would you like to use the suggested settings or keep your current ones?" However, I think this second thing is less important (and possibly harder to implement) than the autogenerated Custom theme.