CakePHP BlueHost Shared Hosting

I am having a little trouble getting my set up and wondered if you could help.

The directory structure is as follows:
public_html/
->App
->Lib
->Webroot

->gallery (non-cakephp)

etc.

I am having difficulty because cakephp has taken over the whole site and I only want it to respond to the main folder but it does it to my subdomain folders as well.

What should I do?

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