I am a bit late on this post - glad to see the answer was simple in the end.
And that is the answer - KEEP IT SIMPLE.
Each axis requires three wires from the computer - a step, a direction and the 0v signal ground - otherwise none of whats follows will see the signal. These need to be identified on the ports and pins and enabled as you now know.
The only problem is you only have 25 wires on the port and 7 of these are 0v signal ground. There are only three sets of usable pins - one with 8 outputs (2 - 9) one with another four outputs ( 1,14,16,17) and one with 5 inputs (10 - 13, 15). If you clutter up your board with nice looking, but useless attachments, you will run out of pins.
If you have four axis (you will probably certainly have three - and at some time want a fourth) that takes care of the 8 outputs in the first set. If you then want M3 M4 and coolant that takes three out of four of the second set and if you want 4 limit switches (with home switches combined) that takes four out of the five inputs - which leaves you one input and one output spare. I have had to compromise because I have a spindle index input, so I only have two limit/home switches. ( I have two spare inputs for something I might find I need)
You do not need charge pumps, and other fancy computerised switches to isolate your axies - this can be more easily done by having an on/off switch on your driver card box - I have one main on/off and then switches to isolate each individual axis ( all illuminated) - and I do not switch the cards on until the computer has run up to speed (as per the instructional video).
About the only other switch I might consider fitting (connected to the computer) is an ALL STOP SWITCH which I shall mount on the machine. Although the computer is next to the lathe, a big push button is easier to hit than a mouse and icon.
The only trouble fitting all these extras ( and I don't decry them at all, I think Mach 3 is the best program around) they all need maintenance - and if something goes wrong in the (I don't know what happened, but everything stopped) category, it is just one more thing to check and test.
If you step over the number of wires on the standard port, then you are into expensive add ons, which, quite frankly I don't consider necessary, and are something to add on when you are up and running and turning out some useful product.
Keep it simple and have fun !!!