I have a similar question.
I am more familiar with WordPress and normally when you have installed a theme, you are informed about updates by the author. You can choose to install this update over your current theme, which will keep your settings intact.
What you are doing is not updating your existing theme, but uploading a new theme and switching to it. And therefore you are starting from scratch.
So how does this work with Template Toaster? How do we update our own theme? Or can we only upload a 'new' theme?