You have 2 wires going into the same cavity of a connector? I am trying to understand wht you are saying. But maybe i can help with just explaining better what those wires are and where they go inside the stepper motor. Inside the motor there are 2 sets of coil windings. Obviously an electrical circuit will require 2 wires to be complete. The stepper driver powers one coil to move the stepper one step, then powers the other set to move the motor to the next step. And the driver is just constantly toggling the 2 coils to actuate the stepper motor. Micro stepping is where both coils are powered up at the same time to create therotecial in between steps. But to keep things as simple as we can here, if you aquired a 4 wire stepper motor without a plug on it as some do come all you would need to do is find the 2 pairs that have continuity so you know the 2 coils and then wire them. If the coils are backwards the motor will move backwards and you can either repin the connector OR just reverse the direction of the stepper in marlin.