The documents found in the Team Explorer menu are controlled by SharePoint permissions. Each document folder in Team Explorer (ex. Project Management) corresponds to a document library in SharePoint. Permissions can be modified at the document library level directly in SharePoint if you have admin priveleges for that site. To do this access the document library that you wish to change permissions for and select "Modify settings and columns" from the left side bar. From the General Settings page select "Change permissions for this document library".
Hope this helps!
Sarah Cameron - InCycle Software