Giving WP its own directory and setting up a Network

According to:

Giving WordPress its own directory will not work in WordPress 3.0 with multisite enabled. It interferes with the member blog lookup. If you wish to install WordPress in a folder AND have that folder name it will work. Domain mapping, however, will not work.

What does this mean? What I want to do is put WP 3.2 into it's own directory (security by obscurity, mostly) and turn on multisite (or network).

Can I do both? I just want to use more than one theme for different areas inside my web site. It is a member web site with different types of users.