The very brief version is, you need to create an init.c file (it doesn't have to be this exact name, but for easy reference that's what it's commonly referred to), which gets loaded when you press the Init button within Mach. Within Mach, the only thing you need to configure are the steps per unit, max speed, acceleration, and the KMotion Plugin. The ports/pins for each axis can be ignored, as that is handled directly by the KMotion/KFlop plugin.
Within in that file, you need as a very minimum the configuration for each channel you'll be using (one per motor), enable them, then using the DefineCoordSystem() function, associate those channels to the relative axis (this has to be in the order of XYZA)
If you look in the C Program folder which contains various example files, have a look at the InitStepDir3Axis.c example file. That is the very minimum you need within your init.c file.
It's probably worth having a watch of this slideshow to get a basic understanding of how things work together - http://dynomotion.com/Help/FlashHelp...ers/index.html
To assist with creating the channel info, you use the config&flash screen within KMotion, along with the Step Response screen (although that may be a bit limited/not needed if you've got no encoder feedback to the KFlop).
Where things get a bit more involved, is your init.c file will typically contain a loop for handling limit switches/E-stops, however start with the basics and expand.
If you're not sure about anything, provide us with some details of how you've got things wired up, and we'll get you going.