At first glance one may say "no it doesn't matter". It is a magnetic switch. I would say that it is a coil that is induced by the magnets in the rotor. Like a dc motor/generator if the field is rotated one direction it produces a + voltage on a specific wire when rotated the opposite direction send the + voltage to the other wire. These wires connect to the CDI. The CDI is looking for a certain type of voltage. Reversing it may cause a problem.
I would connect the wires by using the same locations.
Yes it mattes which way they are hooked up. But if you hook them up backwards nothing bad happens. It just won't start or give spark.
Most aftermarket pickup coils have different color wires than oem. But that's ok. Install it like normal. If you got no spark, swap the wires and all will be well.