It's the one nearest the pedal. If you were to take the MC assembly apart you would find two cylinders in line effectively. The back one has a single pipe running to the back of the car where it splits in two, there are separate outlets for each of the front brakes. Remember to put in a t piece to take the hydraulic switch if you are fitting one, also remember to make provision for the rear anti lock valve if you want to fit one, doing it at this stage is a lot easier than changing it all later.
Details in section 5 of my build diary of you want to see how I did it -
www.deepfolly.co.uk
Dave