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.

Typically, you just run the installer, point to the current, existing StrataFrame db (which has all the meta data for your projects) and run the install. The installer will update the db as necessary, leaving the data alone. I have no idea how many upgrades I've installed since I started with SF, but its been a lot (a dozen at least) and I've never had any issues with the SF database.