Since the SF db contains data specific to my source code, what needs to be done is order to do a SF upgrade without losing my data in SFSProjects, SFSUsers, etc.

The question might be stupid, but I really don't know what to best way to go.

Thanks Greg...as Greg pointed out you ALWAYS want to update the databases with a new update.  We are always careful to never hurt any data that you have created.  At times we update the structures to add new features, etc.