Direct Fire Multi-coil: When wiring the ignition amplifier ensure that the system is wired in cylinder order and not firing order. i.e. Ignition 1 output to cylinder 1 ignition, Ignition 2 output to cylinder 2, etc.
Wasted Spark: When setup for waste spark ignitions, the order of the ignition outputs is simply in the order of the outputs. IGN 1 will fire first, then IGN 2 will fire next etc until the last ignition channel is reached regardless of engine firing order. The following example is for a 6-cylinder engine that fires 1-5-3-6-2-4.

Twin Distributor Ignition: Ignition output will always appear on IGN 1 and IGN 2 channels. In the majority of cases, IGN 1 will be the first output to fire.
Distributor Ignition: Distributor ignition output is always on IGN 1.