For the benefit of future searchers (given the passive agressive lack of response to any theming questions here) ...
This seems to work:
You can set the theme in System > Design. But if you do that and then go changing it and later update your theme, you’ll lose the changes unless you’ve done something like keep it in version control.
So you can make a duplicate of the template directories:
Then below those you can further duplicate the directory tree only to the extent that you need to, to get a parallel location for specific files that you want to change.
Then at System > Design you set your theme to this mostly empty doppleganger theme.
When the system doesn’t find a file here, it will look to the default. But there’s a problem: The default will be the normal Magenta default. So you can rename the default to default_original, and then rename your pristine, untouched version of the theme you’re using to default.
As far as I know, you can’t tell Magento to think of the default as being some other them not named “default”. So you need to rename the pristine theme you’re using “default”. Or at any rate, it will work if you do it that way.
Then you can change the doppleganger theme to your heart’s content. If you update the theme, update the pristine “default” version.
What if an update affects a file you’ve modified in the doppleganger? You’re screwed, I’d imagine. You’d need to track it down, diff it, and update the file where it needs to be updated, but keeping your changes. Some sort of svn version control might help, but that’s beyond me.