I don't understand why every time I go into manage sites and save a site it effectively also gets reset back to the template's menus and default joomla template. Global configs, sitename, meta tags, etc are reset.

If I have a customer that adds some domains that they want to point towards an existing site, adding the sites via site management and saving messes up with the DB, almost as if things are getting re-copied from the template site.

What's the proper way to add domains to an existing site without getting a reset?

When you have define a slave site that is based on a JMS templates, this mean that you use the website configure in the JMS templates to create and refresh your website.

This copy the configuration of the JMS templates website to rebuild the new configuration with the parameters that you have defined in JMS.

If you don't want to have this refresh, you can cut the reference to the original "template site" and say that you want a fresh install.
This will not use the JMS templates to refresh the slave.

Thanks for the reply. It's not very apparent how to update a live site like that. And I'm sure you agree selecting "fresh install" for a live site would not be a choice most would even think to make. IE, that "fresh install" implies the site is going to be wiped out, which I assume is not the case?

Fresh install is the first time.
Otherwise, this refresh the website based on its JMS templates definition.
Therefore, if you don't want this refresh then you have to make it like a fresh slave site (based on nothing).