Depends on what master cylinder you're using. If you have the Corvette style master cylinder, then np, it won't make a difference as that one was designed for 4 wheel disks with the same caliper on all 4 corners. But most disk/drum and even later 4 wheel disk masters will have specific front/rear porting. It's pretty much universal on modern vehicles (I have never seen any exeptions to this) for the port nearest the pushrod end of the MC to be for the front brakes, the other port for the rear.
