Does it matter how the two phases of a bipolar stepper motor are connected?
For example the A4988 stepper driver has outputs 1A, 1B, 2A, 2B. The number designates the stepper coil number, the letter designates the phase.
But steppermotors usually do not show these pin identifiers.
Hi,
This will help;
Because BOTH windings are the same, it doesn't matter what you call A or B coil.
If you get the phase wrong, all that will happen is the stepper will rotate in the opposite direction or not work.
You will not damage anything by getting the phase wrong.
With this driver you need to know the stepper current rating and set that current on the driver.
Tom... 
No.
One way will make the motor rotate clockwise when DIR is HIGH, the other way will make it rotate counterclockwise
That is an issue: for a schematic and subsequent pcb manufacture this statement implies that if a JST 4-pole connector is used with one of the windings "the wrong way" then the motor will not work?
Once a pcb is made based on a schematic there is no way to correct this except to make a new pcb with different coil polarization?
So if both poles are reversed the motor would turn in the same direction?
Yes
Yes there is, you swap the wire connections over where they connect to the PCB.
Or make provision on your PCB to jumper any connections, be flexible.
I hope you are going to make a prototype that works BEFORE going to a PCB?
Tom...
Sure, but me being lazy I even want to pre-empt possible prototype issues 
Hi,
Sometimes that can be called "over thinking" and you need to get out there and build and experiment, like SPACEX, failure is not really a failure, you always learn.
Tom...
@DaveX Thank you, this is MOST helpful!
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