Not sure what kind of car you are working on, but on our '32 chassis, we install tubing down both sides of the frame, behind the boxing plates. You can use these 'tunnel's to run wire for the headlights, parking lights, electric fan, etc. This way you run the engine harness to the engine and its accessories, then the rest of the chassis wiring is concealed.
As far as brakes and fuel, I like them on the side of the rail. Take care and make them flow smoothly, and carefully tuck them up under brackets, etc. Just make sure it looks trick. I tell the guys in the shop all the time to just imagine that a guy from SR or R&C is standing right over you taking pictures..... "Does the work your doing look trick?"