Make your current layout settings (i.e. for your current template) be the default.
You'll get a new button at the bottom of the layout boxes controller screen (admin-_tools-_layout boxes controller)
which updates the layouts defaults to match the settings you have for your current template.
It means that if you switch to a new template, you'll be able to use the reset button (already there) to restore 'your' default sidebox settings.
Important to note: if you have sideboxes installed in one template, but not another one, you will be able to tell in your admin which sideboxes are missing so you can install them in the other template.