Rotary Axis home and/or limit switches

I have added a couple of rotary axis's But am having an issue with coming up with a good way to home them. One switch gives me a home position but if I rotate one revolution the switch is made again. I am using CNCpro, it uses a limit switch as the home switch.(would another program handle this better?)

So for example, an issue on the B & C axis.
Do I home at somewhere >90 degrees then move the B axis to the vertical position once I know what that angle is? Manual Zero this location.
Home the C axis and then rotate it ~180 to find the center of the truncated 360 degree rotation? Manual Zero this location
And on an A table axis I would be limited to less than 360 degrees.

My options are:
Using a M code or manual toggle switch to disable the homing/limit switches after homing
or
Using both home and limit switches, create a logic IC circuit/or PLC that determines conditions.

I've searched but find no info on how this is handled.
There has to be a straight forward way to handle this.
Thanks for any HELP/Direction