The good news is that your alias will not cause a problem, as long as it is simply a URL forwarding to the main site and not a mirror site itself with a redirect either in the form of a meta refresh or JavaScript. If it has its own server, you need to employ a 301 redirect in the form of an .htaccess file. Better yet, just make sure it is only a forwarding URL with no server of its own.

Now, for the bad news, changing the actual domain name of your second site will be painful, especially with Google. By painful, I mean you will drop out of the SERPs on all engines and Google will take the longest to re-establish.

If you can, establish the new domain on another server and, if time allows, use a 301 redirect on the original site that has the domain name you must relinquish. Yahoo and MSN will be quick to respond, but Google will not.

Don't forget to contact the sites in which you have external links to change the link to the new domain name as soon as it's established. Good luck.

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DrTandem's San Diego Web Page Design, drtandem.com