I've gone over a year on the factory filter with the nicktane setup...and I only changed it cause I was worried if the media of the factory filter would eventually break down...I cut it open and it still looked new...
You could run the lift pump between the two filters if you wanted...but the only reason I suggest running it before both filters is the lift pump can fill the filters for you, so in theory...no priming needed.
Plus some lift pumps cannot be run dry...so while you are waiting for the filters to prime with the key on you could run the risk of killing your pump...of course if you keep the factory filter head you can always pump your butt off to prime them...
I never did run the 30 micron w.s. setup as a prefilter to the nicktane...it was to be a good addition to it though...On my build I knew I was going to eliminate the factory head, so I bought a prefilter/water separator to take the place of the factory head...I had a pair of Laing lift pumps and I was going to install the 30 mic and put one pump pre both filters and the other after both filters...the Airdog kept calling my name and $700 later I shelved that project and put the AirDogII 165 on the truck...