The guidance template can't be uploaded "alone" to the TFS, you should upload it as part of project template, for this you will have to download the actual Process MSF Agile (or CMMI) template from the TFS, you can do this from the IDE, just right click in the server name, and launch Process Template Explorer, download it to a folder, and in the directory which has the process guidance "Windows SharePoint Services\Process Guidance" just update with the new one (here it goes the compiled version), and then upload it again with the process template manager from the Visual Studio IDE.
Exactly, there is no way to upload the process guidance. You can, however, checkout the process guidance from the process portal and replace it (upload it). I am looking for a better way than to check out each file and replace it. By the way, it you don't check out the html files, they will not be replaced in th team explorer.
Cheers,
Randy
MSF