Entire site requires login, needs ACL. Where to put authentication check?

[eluser]sneakyimp[/eluser]
Thanks for the very informative link.

I'm a bit confused about 'setting your own prefix.' Why would one want to do that?

Code:

Setting Your Own Prefix

To set your own sub-class prefix, open your application/config/config.php file and look for this item:
$config['subclass_prefix'] = 'MY_';

Please note that all native CodeIgniter libraries are prefixed with CI_ so DO NOT use that as your prefix.

Also, if it's not asking too much, perhaps I could get some advice on my other problem here:
http://ellislab.com/forums/viewthread/238473/