Hello Jerry,
In the Mach3 plugin, you can go to the "Ports and Pins" config. From there, go to the "Inputs" tab. You should see a list of signals which you can tie the device inputs to, as well as an "Active Low" signal for each one.
Basically, for those signals that are connected to Digital Inputs that are active low, you can toggle the signal active low state from here.
-Marc
Vital System Inc.