It is pretty easy to change the process guidance for a new project but a common question that I get is "how do I change the guidance on an existing team project?" I want to start by scoping this post. I am just talking about the html pages or process guidance that exist in the team project. This blog does not describe how to change the work item definitions or reports.
To start, in the Team Explorer, bring up the context menu on the team project that you wish to change. From the menu, choose "Show Project Portal...". When the Project Portal comes up in a web browser, click the "Process Guidance" link on left hand side, in the "Quick Launch" view. When the process guidance comes up, remove "ProcessGuidance.htm" from the URL. In other words, bring up the URL http://ServerName/sites/ProjectName/Supporting%20Files/ in the browser where ServerName is your server name and ProjectName is the name of the Team Project that you want change.
You should get a sharepoint view of the "Supporting Files" directory. In order to change the existing files, you must first check them out. Check out the files that you wish to change and upload the changes. You may want to check them back in so that they don't get overwritten. That's it! If you have the necessary permissions on the Team Portal, you can make the changes. These changes are also visible from the Team Explorer. When adding new files, you may need to leave VisualStudio and reeneter it to see the updates in the Team Explorer.