You always have two different projects: an "initial" .sb7 project and a "web update" .sb7 project. The initial install enables the web update capability. When you have a new version of your software available, you compile a web update project with a higher version number. You upload the new <update>.ini, the web update installer .exe and generated "cluster files".

Similar to this:
http://www.lindersoft.com/forums/showthread.php?t=9459

Does this help?

Friedrich