The password protection just gives you another option besides making a directory password protected. But if your going to use .htaccess anyway, here's a neat little trick that will keep you from typing in your password each time. After you've set up password protection on a directory, go back and configure your .htaccess file like this:
AuthName "Restricted Access"
AuthUserFile "/home/user/.htpasswds/public_html/directory/passwd"
AuthType Basic
Require valid-user
Order allow,deny
Allow from 100.200.300.195
Satisfy any
Just replace 100.200.300.195 with your ip and your ip doesn't have to enter the password, but all others do. This way if your on another pc, you can still access your files with a password.
Or simply not have a password at all and only allow your ip access:
order deny,allow
deny from all
allow from
100.200.300.195