Ideally, what's the best way to route a Series II bass (or any bass) in a rig with an either a mono or stereo preamp and an SF2? The manual shows that the SF2 can either be before or after the preamp... but does it make a difference or depend on other factors?

I have used mine both in the effects loop of an F-1X by 'jumpering' the outputs, (I forget how I did this, but there are instructions) and currently my Superfilter is in use between the output of an F-2B preamp and QSC power amp. 

I remember reading the SF-2 can be used as a standalone preamp as well, but if another preamp is also used there may be some gain issues. 

If you use in the effects loop - keep the SF-2 levels LOW. 

Interesting, i have used mine for years in the f-1x send/return with the input gain and filter gain on full and damping ratio between 1.25 and 1.5. 
The volume on f-1x is usually low and somewhere between 2 and 3 and rarely above that. I run my power amp set at or close to max. Seems to give me a nice clean potent output.
Am I doing it wrong?