Many people including myself find the format of the documentation confusing (especially to start with) however *almost everything is there to be read and comprehended and actioned have no fear the KFlop is capable of almost anything when it comes to motion control of a system!! That said with such a capable system there is some understanding and configuration required.
I would like to see documentation in layers (for me like an IP stack would have been ideal).
I am not likely to be able to help you get your system working, but Tom will help you but you need to consider his time zone (USA), you will find his answers to be like those of a university professor seemingly terse but very educational and informative.
You first need to think about what needs to be wired to what with what sort of electrical signal carried over each wire and select an appropriate port on the KFlop.
It sounds like you just need a step and direction signal initially, there are 8 of these pairs available on the KFlop.
You will probably need to create your own init.c rather than reusing one, the KMotion program can create this for you but this is comes after getting an axis alive.
Have a look at the Step and Direction help file
Step and Direction Setup
You need to choose a physical output connection, and get the wiring in place, the type of output signal from the Kflop ports can be changed there is a table of the options available for each of the 8 outputs. Does your system require LVTTL signals or Open Collector? I presume you have a servo driver that will need these, but I would also presume that the servo driver needs an encoder for feedback but it is a long list of questions and I am only typing this as I am avoiding doing things that I should be doing ;)
The Config & Flash page in KMotion can be used to configure each axis (start with just one) this configuration can be downloaded directly to the Kflop and it can be stored in a configuration file, but you can get it working without creating an init.c file initially by using the "Download Channel" button.
Then you need to use the Step Response screen in KMotion to test if you have got it right, if you have you will get some motion on the axis being tested.
There is no point in trying to use KCNC or Mach3 until you have a physical response when you use the Step Response screen.
When you have got an axis working you can then think about storing that configuration in an init.c file for use from then on, as you configure more axis you add the configuration for each to the same init.c file.
I hope that helps you focus in the right area to start with, there is a lot of learning but it is very worthwhile.
Good luck.
Jon