The front pipes must go to the rear piston i.e. the one closest to the pedal and the rear brake line to the front piston. The reason for this is that the rear piston has only a hydaulic connection with the front piston so that when you press the pedal the rear piston pressurises its circuit and then pressurises the front piston. Usually the front brake pistons are larger than the rear so that the front brake m/c piston needs to move further potentially that the rear piston. If you plumbed it the otherway round the rear brake would hydraulically lock everything up before the front got to anywhere near its full travel.
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