There are many ways you can set this up, I will give you the method I have done in the past on my Mustangs. Basically you will need to install the FMU on the return side, usually after the universal fuel pressure regulator. I run -8 fuel line from the pump to a splitter that splits into two -8 lines that go to rear of the fuel rails. On the return side I come off of the front of both rails with -6 that goes to the regulator then out the regulator with -6 that goes to the FMU and then to the tank. This was a basic design that Aeromotive gave me a few years back. I use it without the FMU on my 94GT at this time.
Take care,