I assume if you're using it with Mach3, you use the usual ports-and-pins mapping page. Don't know about UCCNC as I've never seen it. Guess that there's an equivalent set-up screen?

Trouble is, put all the detail in the manual and you confuse people. Don't put in every last detail and someone will bitch. Best bet is probably put in enough for someone intelligent and knowledgeable, and kick off with something like, "if you don't understand this, ask yourself if you should be doing it by yourself. Why not ask someone who does know what they're doing?" Actually, that's probably where this forum kicks in!