DevShed.com has the newest part of their paperless with PHP articles up this morning, Cracking The Vault (part 2). While the first part when into some of the setup issues and theories behind it, this one gets a bit more in-depth into the stucture and function of "the vault."
Also, the NewbieNetwork has a nice link this morning to a great seach tutorial that gets into using a search for your "complex website." Hmm....maybe I should finally add a search on here.