The quick rule of thumb is if there is a place to change a setting in the SmoothStepper configuration then that is where it needs to be set. As I understand it there are a few settings that Mach does not notify a plug-in when the setting is changed so they were added to the SS config screen, the SS also allows you to set the 'debounce'/'noise filtering' by input type so you can have different settings for limit switches, than a probe, than EStop, etc.