After many hours of trial and error do to no paper work here is how you do it.
Limit switches- these are wired in series, you need a switch per axis wired to a ground and to the "limit" terminal. You can use this without using home switches BUT you can only home in the "homing Sequence using "zyx" or "zxy". How it works- when you hit the "home" button the machine will home one axis at a time, when the switch hit than the next axis will start and so on. You must have the "home using Lim" checked off in the "deskcnc setup tab.
Home switches- These are wired in parallel with the ground wire. Very important you must have the "home using Lim" un-checked in the "deskcnc setup tab. On the Machine tab you can select "simultaneous" for homing sequence. The switch for this will be normally closed, so as the machine homes and hits thw switchs the board sees +5v and goes on to the next axis.
The above maybe revised, I have to double check all my facts but this will help many that have no direction.