This setting doesn't really have anything to do with the way you arrange the effects within your scene. Since you can put any effect in any slot in the M9, you can put your effects in any order you want. What the 1<2<3 or 3<2<1 setting does is determine how the signal flow goes through the pedal itself. The default is 1<2<3, but going left to right is the opposite way most people have the signal going on pedalboards. Almost all pedals have the input jack on the right side of the pedal and the output on the left. So the signal ends up going from right to left. Setting the M9 to 3>2>1 will make it so the effect in slot 1 is the last in the M9's signal chain. Flipping this setting won't actually change your tone at all, though. The M9 automatically moves the effects that were in slot 1 to slot 3 and vice versa.