Is there any difference
 

Between reversing the motor wires or changing the direction in the Castle Link program?

no difference

There's a difference, if your direct soldered then it's a hell of a lot easier to change it in the programming. If you use bullets, it's easier to swap the wires. :intello: :na:

From an operation standpoint, there's no difference. However, if you want a specific color order for aesthetic reasons, then the easier way is through software.