You have to tell the drive that you are using Step/Dir inputs, see first screenshot.
Next you have to tell it if you want any gearing between the step inputs and what the drive sees (second pic). For example if you are just using the parallel port then you may not get the spindle turning very fast due to the pulse limitations of the parallel port and the kernel you have set. So what you would have to do is set some gearing in the first box. If you had it 1:4 then what the drive would do is multiply every pulse from Mach by 4.
As far as the inputs for the Step/Dir they are on specific pins, 4,5,6,and 7 if I recall. You may also need pin 2 connected to the same Gnd that your differential signals are connected to.