The easiest way at the moment is to install the same theme twice and change the palette (and also the theme name, so you know which is which).
It’s easier if the theme is remote (on git) because then all updates are centrally managed anyway. If the theme was built locally in the admin interface you can export it and re-import it. The local theme method is a little more annoying because you have to edit both themes if you want to make any changes.