Sending a pulse to the step pin is not a place where you would be using PWM -- or certainly not where you're using step rates of 10 steps/second. The A3977 does specify a minimum pulse length of .1 picoseconds but that length of time is shorter than two consecutive calls to digitalWrite() and is not a concern.
As previously suggested the BlinkWithoutDelay example should give you the foundation you need. With respect to interference with serial input/output it is important to keep your messages short, however, but still not likely to cause great concern while keeping pace with a slow step rate.