Put the home switch where you want the home position to be located. let's say for the x-axis it's the left hand side at 0. Put the overtravel limit switch at the extreme left just before the mechanical maximum negative travel. This could be at -.5" or whatever. If there isn't enough room, you could stack the switches on top of each other and have them staggered just a little so the overtravel switch isn't hit when homing.
Eric