I had the same questions when I was installing my FASS.
I did not alter the stock fuel delivery system, much. I cut the ground wire to the in-tank pump and soldered in a fuse holder that I can access easily without dropping the tank. If I ever need the in-tank pump again, I drop in a 20 Amp fuse and off we go. I then removed the fuel feed line from the back of the stock fuel filter. I plugged the banjo with a bolt and a couple of new crush washers to keep debris out.
I installed the separate pickup line to feed the FASS. All the replies I got on this forum indicated the stock feed line would not provide adequate flow. I did all the other plumbing per FASS instructions except for where I deliver fuel to. I have the feed line from the FASS entering the back of my stock fuel filter. Now I realize some people are going to wonder why I'm putting fuel thats been filtered to 3 microns through another filter that only goes down to 7 microns. Ease of installation mainly, but the installation from under the hood looks stock as the changes I've made are in behind the stock filter.
Overall I really like my FASS. In my Mega Cab with the doors closed you can hear a faint hum with the ignition on but when the engine is running any noise from the FASS in drowned out by the engine.