Usually it's however you see it fit to lay out what you need in an easy-to-understand manner.
For example, the vBulletin administration pages have a side navigation on the left, and the content on the right. At the top of the content is a small little bit denoting the current forum version and the most recent code available from vB.
A project I used to work on had about 5 buttons in the admin panel, and that was it. You could choose from 5 things to do (add stories, add photos, update stories, etc.).
It doesn't have to "look" like anything if you don't want it to. Half of the challenge to putting together a good PHP application is user interface. How can you best design your program so that a user can seemingly "just know" how to do what they need with little reliance upon the help functionality.
