Setting up addon domains properly (bonus duplicate content issue inside)

[Mattymar]

A new client of mine is using 1and1 hosting from back in the dark ages.  Turns out, her primary domain and her main website (different domain) are exactly the same.  She likes to have the domains names of her books, but her intention is to have it redirect to her main site.  Unfortunately, 1and1's control panel is light years behind cpanel, so when she set up her new domains it just pointed everything to the same directory.

I just want to make sure I don't make this up, so please correct me if I'm wrong about something.  I'm assuming this is a major duplicate content deal, so I plan to create a new directory for each add-on domain.  Since her main site is an add-on itself, I'll have to move all the files into it's new home directory.  Then I'll create an htaccess file for each domain and redirect it to her main site.  Right so far?

My major concern is with the duplicate content.  She's had two sites being exactly the same for years.  Will there be any issues leftover after I set everything up properly?  Is there anything else I need to do?

Thanks for the help guys! I'm fairly new to this community and love the opportunity to learn from the best!

[Mattymar]

Thanks a lot Chris, that definitely helped.  Bit of a messy situation, but I'm glad that things should go a lot better once it's all cleaned up.

[Chris.Menke]

Mathew,

It sounds like you're on the right path.  In cases where dupe sites have existed for a long time, there may be external links pointing to both sites, so you want to survey back links. If google analytics is installed on the domain(s) to be redirected, be sure to note which pages are bringing traffic from search.  Redirect pages with back links and those getting search traffic to the appropriate domain.

Depending on the circumstances, after the settling-in period, you could see an increase in rankings for the main domain.  If she's a local business and has all of her local citations set up, it would be good to make sure all of them reflect the proper domain name.  Also, attempt to contact sites with links pointing to her old domain to see if they'll update the links.