Proper Hosting Setup to Avoid Subfolders & Duplicate Content

[ATMOSMarketing56]

I've noticed with hosting multiple websites on a single account you end up having your main site in the root public_html folder, but when you create subfolders for new website it actually creates a duplicate website:

eg.

http://kohnmeat.com/ is being hosted on laubeau.com's server.

So you end up with a duplicate website: http://laubeau.com/kohn/

Anyone know the best way to prevent this from happening? (i.e. canonical? 301? robots.txt?) Also, maybe a specific 'how-to' if you're feeling generous

[JohnW-UK]

I have the same problem with so of the sites I manage. Luckily the search engines have never found or indexed the duplicate url i.e. domain.com/secondsite. Have the search engines indexed it for you? If not is it really a problem? I have considered a 301 or robots.txt but due to it never being found/indexed I did not see the point.