Carrot30,
When migrating from Windows Vista to Windows 7 you will have the option to select "custom" or "upgrade" install when prompted. By selecting the "upgrade" option, your documents and applications will follow and carry over through the install process. If you select, "custom" however you will be able to perform a clean install and all applications will have to be reinstalled manually -- documents will be moved to a folder entitled "windows.old".
For additional assistance with the migration of Windows Vista to Windows 7, Microsoft does have an official Windows 7 Support Forum. It is supported by product specialists as well as engineers and support teams. You are welcome to check the threads there and receive additional assistance and feedback.
Jessica
Microsoft Windows Client Team