Inventor is capable of creating complex 3D assemblies. These assemblies are made by combining various part files that are either custom to that assembly, or that are shared across many different assemblies. This collection of files must be organized in such a way to make it easy for the designer to use. Inventor does this by creating what's called Projects.
A Project organizes your data by creating a Workspace which is a series of directories (folders) that all the custom parts and drawings are located for a given assembly. Some Workspace directories may be stored locally on the designer's computer, while others may be stored on a server allowing others to work on them at the same time.
Oftentimes there are many part files like fasteners or bearings that tend to be reused across many assemblies. These part files are stored in folders that are referred to as Libraries. Since Library parts are shared across many different Projects, they are not allowed to be edited.
Autodesk has been moving toward using a program called The Vault to store Inventor files. Inventor R12 (2008) no longer allows Projects to be multi user unless all the files are stored in The Vault. The Vault handles file management in a multi user environment better than Microsoft's NTFS file system, eliminating many issues that used to plague Inventor.
A good starting point for projects is the Autodesk Inventor Project Files Revisited document.