You set the step frequency for any axis you are using to what you need or the setting just above. For example you may have 100,000 steps per unit and a velocity of 100 units per minute so that would equate to you needing 100,000 x 100 = 10.000.000 pulses per minute so 10,000,000/60 = 166,666 pulses per second (or Hz) so divided by 1000 would give you 166.66KHz so you would choose the nearest above that setting which would be 256KHz.
Do that for each axis you are using and any axis you are not using set it to the lowest (32KHz)
Spindle will be whatever you use and is relatively self explanatory with maybe the exception of the pulse width if you have a Step/Dir spindle. For that it will depend on the steps per rev you have and you may need to lower it to obtain full speed.
Miscellaneous is more or less self explanatory except the number of data points, probably best to just leave that as default.
M11/M10 is if you are using that function for a laser so if you are not then no need to set that.
Noise filtering will be left at zero unless you have issues with false triggers then you can try a small amount of filtering for the problem input, dont go too high though or you may have more issues.
Pins 2-9 just determines whether you want them as inputs on ports 2 and 3 or set as outputs as they would normally be on a parallel port.
The monitoring doesnt need anything done, its just there to see whats happing if you have issues.
Hood