Maybe with some descriptions it's a little easier to follow...
Unlike most petrol engines, a diesel has a fuel supply line, to either the injector pump or the common rail primer pump, and a return line back to the tank.
My OEM fuel filter has 4 connections (2 ins and 2 outs):
* in for fuel from the tank
* out for filtered fuel to the primer pump (then to the common rail high pressure pump)
* in for bypass fuel from the primer pump
* out for fuel being returned to the tank.
The fittings on the OEM filter are 10mm for fuel going to the engine and 8mm for fuel being returned to the tank, so it is easy to see which line is for which. There are also arrows on the OEM filter housing indicating the flow direction.
The additional water trap is simply fitted between the tank outlet and the OEM filter.