I'm documenting WAS 6 issues. I've already discussed Keeping WAS Up-To-Date. There's also a tool for installing patches into WAS.
The IBM Update Installer for WebSphere Software is a wizard that takes the patch files (aka interim fixes, fix packs, and refresh packs) and adds them to your WAS install. "Update Installer for WebSphere Application Server V6.0 releases" (Reference #4008401) and "Update Installer for WebSphere Extended Deployment V5.1 releases" (Reference #4008546) have more information about the Update Installer and links for downloading the latest version of the installer.