Hi James,
The portal manager doesn't quite work the way I think you are wanting it to (and the way I wanted it to). On the left are "application" tabs where I think you may be wanting them to be more like catergories. There was catergories in the old Desktop manager but they have now changed to filters on the right-hand side. The applications tabs on the left can be configured in the portal manager settings found under toolbox item "agent settings", in the console. In the middle you will have all the software distribution tasks based on "Optional" or "Recommended" type policy based delivery methods. The difference between the two being whether or not the software is ticked by default when opening portal manager. Also in the man launchpad tab will be any launchpad links that have been deployed to the device.
Moving on to how we use it... We have all our links and free applications listed in Launchpad tab and are looking at implementing a couple of applications down the left to do things like common forms, computer deletion tool, force patching scan and repair.
Hope this helps. I can get screenshots if you like but I haven't put them in because we have a bit of branding on there.