Can I have separate passwords for each Alias (folder) and/or just protect select folders?
Not directly, but yes. The build-in password authentication system does NOT support multiple passwords or usernames, additionally, it does NOT support per-folder authentication, but you can use a PHP or other CGI based authentication system. This system must not use HTTP authentication but must use a login based system, such as that of phpBB. Do a search on the Internet for information on “PHP authentication”. Note that PHP (available from www.php.net) is required before you can use PHP.