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I think I understand better now.

Use the noindex,follow tag on the content you don't want included in the search index.

If you are using Wordpress then you should check out http://yoast.com/wordpress/seo/

In the campaign section you paste in keywords separated by comma tab or newline.

<embed id="Siber_embed1" style="left: 0px; top: 0px; width: 0px; height: 0px; position: fixed; display: block;" type="application/rf-np-plugin">

You can see it here:

http://royaloakshomesfl.com/robots.txt

So its in the webroot of your hosting.  You can change it via FTP to and change it to the following to grant full access until you have figured out robot access rights.  I think you need at least one Disallow: line without the / slash in your existing configuration to make it work.

User-agent: *
Disallow: 

One take on this would be to add a 301 redirect one of the URLs onto to the other.  As Vjay mentioned this would look after any inbound links to the page.

this post has some good info also

http://www.seomoz.org/blog/301-redirect-or-relcanonical-which-one-should-you-use

Hi,

If you have access to GWT for the domain you could use the 'Fetch as Googlebot' tool and check out the how it fetches the page and data it downloads.

Hope this helps!

Now that the new site is ready maybe you can move it out of its set-up directory into the root domain?  I'd also set-up 301 redirects so the pages from the old CMS are forwarded to corresponding pages on the new CMS

www.yousite.com/blog/story1 >>301 redirects >> www.yousite.com/news/tech/story1

Is it a problem if http://www.mydomain.com is not optimized for anything?

The root domain is forwarded onto the directory with Joomla install so you can't optimize it for anything.  If you keep it like this make sure its a 301 redirect.

Hope this helps.

Hi there,

You have to verify the sub domain e.g. www.domain.com and the root domain e.g. domain.com.

If I recall correctly to do this you just add another site within webmaster tools and verify it.

Hope this helps.

Yes that's correct.  So you will have 2 sites added to GWT - your-domain.com and www.your-domain.com

Hi,

301 them to corresponding pages on the new site if possible.