Well, in interests of getting some content on this rather dead blog, I figured I should post what I just figured out in terms of how to setup a .htaccess file to handle a website that actually setup in a subdirectory under the main webroot directory.
My own personal solution to organize my sites
/
/404.php
/stage
/stage/index.php
/test
/test/index.php
/website
/website/index.php
Basically, /website needs to act as the "root" site, but going into /stage and /test should be allowed. This was to provide a separation of webroots, but here's the .htaccess file that seemed to work with how I needed to work:
# Set the 404 page
ErrorDocument 404 /404.php
# Turn on Rewrite engine and set base
RewriteEngine on
RewriteBase /
# Rewrite root directory to subdirectory
RewriteRule ^$ website/ [L]
# Check that the request is not an existing file or directory!
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
# Ignore the target directory
RewriteCond %{REQUEST_URI} !^/website/
# Ignore other directories at root (must manually add another line for each of them!)
RewriteCond %{REQUEST_URI} !^/stage/
RewriteCond %{REQUEST_URI} !^/test/
# Do the redirect
RewriteRule ^(.+)$ website/$1 [L]
Basically, any access inside /test, /stage, and /website will be left as is, but any other access will be a) checked that it doesn't already exist as a directory or file yet, if not, then website/ will be appended to the begining of the directory behind the scenes. Basically, /index.php would be rewritten to /website/index.php, /thisdirnotexist/thisfilenotexist.html is rewritten to /website/thisdirnotexist/thisfilenotexist.html, but /test/notexisting.html would be left alone.
Hopefully this helps others.