Checkout Wizard File Creation problems

This is probably a really stupid question, but I am pulling my hair out trying to figure out why the Wizard is putting the files in the locations that it is putting them in.

I have my setup so that dreamweaver logs into my root directory, which is where my public_html folder is for my public site. I have it setup this way so that I can see the files that are in the root directory. The root directory also contains the WA_eCart folder that contains the configuration file. When I run the wizard, it asks for the directory that I want the files in ie: public_html/cart/. It creates folders in the strangest places. How am I supposed to have it setup so that it will put the files in the folders that I specify. I don't want images and CSS files in the root directory, as they cannot be accessed from within the public_html directory, but I don't want my config files, and files with passwords in the public_html directory. I am lost!

Thank you!

You would probably want to define another site that is already in the public_html root directory.

The wizard will always create the folders in the root directory of the Dreamweaver site, so you'll have to set it up to already be within the public_html subfolder in order to have it work properly.