Multiple Domains Issue

[kdobson99]

First, treat me like I am an idiot, because when it comes to things like robots.txt... I am.

Here's the problem. I have a top level domain on my shared hosting account that I don't use.... say www.mysite.com. But, one of my add-on domains, say www.example.com is a site that generates a lot of revenue (thus I obviously don't want to mess anything up here)

Technically, the add-on domain is a subfolder of the toplevel domain, so you can access this page: www.example.com/page1.php alternatively by this url: www.mysite.com/example/page1.php.

Unfortunately, for a few pages google has started listing some of the pages meant to be a part of the second level domain as part of the top level domain.

But I'm afraid that if I put "noindex" in the robots.txt file in the top level domain (mysite.com) that it will also prevent the indexing of the add-on domain (example.com) also. How do I solve this?

[DavidAtWork]

Have you been able to confirm that google is also showing "www.example.com/page1.php" as well or is it just showing "www.mysite.com/example/page1.php"?
My thought would be that if it has indexed both versions then it has indexed it as two seperate web sites and therefore it would be ok to place the "noindex" in "www.mysite.com/". I have never had this situation, however, so wait till someone else confirms. This is just my opinion.
D

[kdobson99]

For some pages it displays one, and for others, the other. At some point I must have had a link that went back to the top level domain on accident, so now, when I do a "site:" search for the top level domain, it returns about 170 pages that are located in the folder with the name of the add-on domain. Whereas the add-on domain has about 3,000 pages indexed. However, I'm just afraid google will keep indexing pages from the top level domain as well and want them to enter from the add-on domain instead.