Recommended Directory Structure

I normally put files for a GoLive Project I'm working on in the directory above web-content, web-settings and web-data.

I just noticed that for VQ projects, if I put files into the directory that contains documents, web-content, web-setting and web-data, they are included in the project.

Is this the normal behavior?

To keep files out of VQ, do I need to nest the site an additional level?

Example:

This directory structure to keep the files out of VQ that I don't want managed...




e:\site\ABC\asite\asite on 127.0.0.1
e:\site\ABC\asite\asite on 127.0.0.1\documents
e:\site\ABC\asite\asite on 127.0.0.1\web-content
e:\site\ABC\asite\asite on 127.0.0.1\web-data
e:\site\ABC\asite\asite on 127.0.0.1\web-settings
e:\site\ABC\asite\notes.doc
e:\site\ABC\asite\code.php
e:\site\ABC\asite\data.xls




Instead of this, which keeps files out of a normal GoLive project, excluding the documents directory of cours...




e:\site\ABC\asite on 127.0.0.1
e:\site\ABC\asite on 127.0.0.1\documents
e:\site\ABC\asite on 127.0.0.1\web-content
e:\site\ABC\asite on 127.0.0.1\web-data
e:\site\ABC\asite on 127.0.0.1\web-settings
e:\site\ABC\asite on 127.0.0.1\notes.doc
e:\site\ABC\asite on 127.0.0.1\code.php
e:\site\ABC\asite on 127.0.0.1\data.xls