The ribbon cable is used to connect one KStep using JP36 to JP7 on the KFlop, so that KStep uses step/dir outputs 0-3.
The short RJ cable is used to connect the other KStep JP26 to KFlop JP5, which means that KStep uses step/dir outputs 4-7.
I'm guessing going by your description, the cable lengths are designed so that if everything is stacked, the bottom KStep uses the ribbon cable, and the top (middle card in the stack) KStep uses the RJ cable, with the KFlop on top.
You also need to provide power to the KStep connected via the RJ cable, which can be done by using some short bits of wire to loop between J6 on both KSteps.
Thanks I think that makes sense , as I can visualize it in my head .
I was planning on having 5 volt board power through the USB on kflop board , and thus the ribbon cable kstep so I should be able to connect the 2 kstep boards through j6 , but do I remove the j3 jumper on kflop ?
I read the manual multiple times but but the j3 jumper eludes me in my application
Also the j6 is not actually numbered on the kstep connector pinout photo on the website so I assume it is the 4 pin terminal block direct above jp31 and jp32
If you are powering everything requiring 5V via USB, then you need J3 installed. With it removed, it basically disconnects the USB 5V, so the KFlop has to be powered from an alternative 5V source. It's discussed at the end of the text description for JR1.