I have been working this week on setting up Team Foundation Server for a client and have also been investigating the use of the Scrum 1.0 Template for TFS. In working through the installation, there were some considerations to think through when setting up the initial project structure.
Microsoft has some good resources on how to go about Planning a Team Project, including a good flow diagram that asks relevant questions about your setup. Questions such as how many people will use the system, how many projects there will be and thoughts about what type of software development process will be followed.
Team Project Collections
With TFS 2010, a single server can have more than one Team Project Collection (TPCs). One TPC is a group of Team Projects, and each TPC is completely separate from another TPC installed on the same server. TPCs also have completely separate defect numbering systems, changeset numbers, work items, etc. Things in TFS 2010 are identified by team project collection in addition to server url and item ID.
You can read more on this at the excellent TFS 2010 Key Concepts blog post.
A TFS Team Project is the child of a TPC, and it contains the logical grouping of all elements that comprise a software application. Minimally, the tools and artifacts required to develop the software application are contained here. In addition, a team portal, source control policies, and reporting site are available. When you set up at Team Project, in addition to naming and describing the project, you will be asked to select a process template for the project (such as the Scrum template); this will dictate what development process tools are available for the project.
Here is a link for more information about Team Foundation Team Projects.
TFS Installation Guide
The TFS Installation Guide for Visual Studio 2010 is a good resource for getting started. Note that in order to actually use this download, you must right click the file, select properties, and then click the Unblock button in the General tab.