I'm not sure what you mean by microstepping in repetier. Microstepping refers to a setting on your stepper motor driver board that is typically not controlled by software.
Are you talking about "infill ever N layers"? That is a function where you can have your outside perimeter be, say, 0.1mm, and your interior be 0.3mm, because only the exterior layers are seen. This saves on some models a lot of time. You should be cautious if your speed settings are set so that the infill is done much faster than the perimeters, then you might reach a volume-outflow limit for your system. In which case you could find the quality or likelihood of problems to slightly increase on the infill.
Anyway it's a setting especially useful if you have a larger model (it makes less of a relative difference to a small model.)