Can I set up a master project on my desktop and have sub projects in various folders under a single site on SharePoint?
Answer: The problem with Master projects is that Project will not allow you to connect the Master to sub-projects on SharePoint. To work around this, you can check out the sub-projects to you local drafts folder (My Documents > SharePoint Drafts) then connect the Master project to the local version of the file. When you’re done updating, simply check the files back into SharePoint to save any updates.
