I take it back. If you put the project and it's media in a single folder, import that as a Bundled Asset.
We are working with AE in a different way:
1. Before starting a AE project make sure all of the assets are already in FCSvr.
2. Start an AE ( I would assume PP works the same) project, and just drag and drop assets from Final Cut Server.
3. Finish your project and check into FCSvr. Now anyone on FCSVr with edit-in-place access to the share ( eg. Xsan ) can check out those projects and continue working
Of course, you don't get extra benefit of working with FCP6 or 7 projects, such as modifying access date on each linked asset, not warning if an asset is missing or archived, and finally no pretty icon. But you can at least create a custom metadata group for AE and PP projects.
If you already have completed AE projects, I had a following workflow to bring them into FCSvr. Place the AE project consolidated folder on a file based device, and run a scan to catalog all the media except the AE project. Then open the AE project from this folder and re-save it on your desktop. After that check into FCSvr: voila, it will keep all links relative no matter who checks it out.