Pololu A4988 Decoupling Capacitors
I've already got a 100uF cap across Vmot/gnd, but there's the 5V logic
  Vin/gnd.... should I put a decoupling cap on that, as well, since it's
  coming from the same power supply?


The caps function like a current 'buffer', they source current when it get's too low and sink current when it get's to high to maintain a constant voltage level. In the example below L1 and R2 represent the wire, C1 is a filter capacitor and R1 is a variable load.



The reason for using capacitors is the instantaneous current switching that circuits with millions of transistors can have and the other problem is that wires have resistance and inductance. If you could measure the inductance and resistance of the wires, you could actually tell how well of a filter you've built. 

But for most of us we just 'ballpark' the capacitance, because that saves time. 100uF might be a little steep, and might increase the start up time but should be fine for your application. Digital lines are an important place to put caps on due to the variable nature of the load. Motors, especially stepper motors are another good place becasue they also switch, so I'd put caps on both.