Exclude password protected folders using .htaccess

How can I exclude individual folders using .htaccess?

For example I have WordPress 3.0.1 MU installed in the root of the domain using subfolders, not subdomains.

I have Joomla installed in a subfolder and want to password protect the administrator folder for extra security.

When I use .htaccess in that folder to do the password protection, WordPress throws me back to the front page and the protected Joomla admin folder is inaccessible.

I am guessing I either need to add some code to the .htaccess in the Joomla admin folder, or to the .htaccess of main WP MU install, or both.

I’ve tried the folder exclusion codes recommended by people on the Internet but they either have no effect or get me a site-wide 500 error.

If the main site is /home/mysite/public_html the subfolder is /home/mysite/public_html/joomla and the password protected folder is /home/mysite/public_html/joomla/administrator where the domain is http://www.mysite.com what code should I use to get WPMU to let me both password protect and access http://www.mysite.com/joomla/administrator ?