WSUS 3.0 delivers updates to corporate environments from Microsoft Update.
This readme file describes known issues affecting Microsoft® Windows® Server Update Services 3.0 (WSUS 3.0) and includes recommendations and requirements for installing WSUS 3.0.
The documentation for WSUS 3.0 on SBS 2003 R2 will be out soon, but the key thing to remember is that when you install it on top of R2, you don’t run the wizard. Just install it over the top and don’t change any of the settings. WSUS 3.0 will be controlled by R2 just fine.