Changes through the Template editor not showing on the site
Using Jamroom
Only the native skins would get updated, so your clone skin(s) are safe. That is the idea behind cloning them.
When using the template editor, changes are saved on the database and not in the template file. That is why you then have to enable the edited file. Disable it to revert to the original file. This also means that you can compare the original and edited versions using the tool alongside each template. Again, using this method, updates to the original templates will not affect your changes.
Note that if you clone a skin with templates edited via the ACP, those changes will go into the cloned skin so that you could 'stage' your skin development doing this, and revert to a previously cloned skin if things go wrong.
Yes, the ACP editor is a bit clunky compared to other more featured ones, but you have the choice of what to use.
hth