The larger-volume reservoir needs to go to the disc brake system because it takes a lot more fluid to make the large caliper piston move, and there might not be enough fluid to compensate for pad wear if the small chamber is used. The smaller of the two chambers will handle the smaller-volume wheel cylinders of the rear drum brakes. If it's got equal-volume reservoirs like some of the early drum/drum systems had, front to rear hookup won't matter as long as the drum system plumbing gets a 10 pound residual pressure valve. 10 lbs. on a disc caliper will make the brakes drag. It's needed on a drum system to keep the fluid pressurized against the tension of the shoe return springs.
As long as there's a full column of fluid between the M/C pistons, they will move together as the brake pedal is pushed. It's when the fluid between the two pistons leaks away, or air gets into the system that pedal height becomes an issue.
Jerry
