Please help.

I edited the template to make a copy of a new slave site.
I created a new site. and now all sites are exactly the same.

When I go into Global Configuration they all share the same DB prefix.
If I edit the prefix to be correct to that slave site. All sites get updated
to the same DB prefix. Please help!

When you see the same site everywhere, that would probably means that you had an error when defining (saving) the slave site definition.
In that case, when an error occurs, JMS does NOT update its master index and when the URL is not recognized then it display the master.

This is the reason why the website display the same content with same DB and prefix.

Therefore, cross-check that you don't have any error when creating the slave site.
Also verify that all the patches are installed.