Ok I see nobody is answering the question. It does not matter I figured it out after a week of tinkering with it. I selected the second diagram and setup where I used one pin input for each axis for the homing, ++ and -- limits of each axis. It homes now nicely with limit switch protection. So if anyone ends up having the same dilemma, and that is to know how to best connect limit and home switches, you could find this post useful. Thanks