If you know the pinouts then it should be a simple matter of asigning them in Mach, just make sure you choose the Sherline 1/2 pulse mode. You will see all the pin options and Sherline option from the Config menu then Ports and Pins.
Mach can only control axis over USB if there is a motion control device with a plugin, there are a few such devices, SmoothStepper and DSPMC being two of them, if however you are running EMC from the parallel port then it would seem prudent to run Mach from that also, at least for the time being.
Hood