There is no need to change the connection strings of all the domains of your customers. Only the server localhost has to be replaced with IP or the servername of your new mysql server. That's it and you are done .
I am intrested in setting up a second server to just run mysql for my site.
Now would there be a way to set it up so that all users scripts who set there mysql scripts to connect to "localhost" to be automaticly redirected to "what every ip the mysql server is"?
Yes, quite easily via iptables. Ask your sysadmin to set it up.
Hopefully you do realize that there won't be any cPanel synchronization of MySQL usernames/passwords/databases on the second server. For this you'll need custom hacks, probably a MySQL clustering kind of solution. This, of course, is why people write their own control panels instead of relying on off-the-shelf panels which don't support clustering.
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