The process flow for managing 3rd party updates with Configuration Manager 2007 is this:
1. Select updates for publication to the Software Update Point and publish.
2. Synchronize the Site Server to the Software Update Point to get the Update Repository populated with the newly published updates. (Note: If the updates published are the first ones for a Vendor or Product Category or Update Classification, this synchronization will only update the products & classifications list. A second synchronization after enabling the desired Vendor, Product Category, or Update Classification will be required.)
3. Add the updates to an existing Deployment Package, or create a new Deployment Package.
Also available for deploying 3rd party updates to ConfigMgr clients is the Patch Manager Update Management Wizard. Please see this blog post for an explanation of that capability.
Expiring updates generally will happen automatically as a superseding update is published to the SUP from Patch Manager; however, if you wish to explicitly expire an update, you can do that in the Patch Manager console.