I have a under deck tank (12 galls)with water seperator/filter in the consul. I also have a 5 gall plastic tank that has it's own fuel line, primer bulb, engine connector. which I fit to the front of the consul with a ratchet-strap. This arrangement:
1. Keeps the weight of the spare fuel forward and helps balance.
2. Ensures a completely clean supply of fuel should there ever be any contamination of the main tank.
I don't think you need to worry too much about having the water seperator filter in-line with an aux tank as I think it is meant to deal with the main tank only - condensation, etc.
The engine will have a filter fitted internally I would think so this would take care of the fuel from the aux tank.
Peter (nick, nick) T
Age and treachery will always overcome youth and skill! Bullshit and brilliance only come with age and experience.