OK, Loui
Under Config, Ports & Pins, Motor outputs, Have you assigned a Port # 1 to all Axises, Step/Dir Ports. Right side of window and Apply.
Same window, Changed the Dir/Step Low Active to different State.
Same window, Inputs Tab, Set up port Pins for your axises, changed the Active Low State.
Diagnostics Page should show switch activity when Pressed.
Take a Look, Chip