The pins on the SS are like the parallel port, in other words on Port 1 you have 1 to 9, 14, 16 and 17 are outputs and 10-13 and 15 are Inputs. Port2 can be either the same as port 1 or you can configure it so that Pin 2-9 are Inputs rather than outputs but all other pins remain the same. Port 3 has 5 inputs 3 of which are differential so can be used for encoder/MPG inputs if your encoder MPG is differential.
As for which Input or Output does what, well that is up to you and you just configure that in Mach, for example if you have limit switches connected to Port 1 Pin 10 you just assign that in Machs Ports and Pins, Inputs page.
Hood