If that`s the case, how would you set mach3 with appropriate directions of travel
You can't change the directions of travel. Mach3 uses the Cartesian Coordinate System, and each axis has to move a specific direction relative to the others.

Now, you can have the machine home to anyplace you want. to do that, use the Home Offset settings and use the Home Negative option to make sure the machine travels in the correct direction to find the switches.
I have my X axis home offset set to 45, and home to the positive X direction. So my home switch is at X = 45, and machine zero is at the opposite end from the switch.