Mach's setup screens can be very confusing. The green check mark = active low, the red X = active high. This is true for the input pins and the step and direction pins. For example, if your limit switch goes from high to low when triggered, it is "active low".
And now for the "native units" setting.
I use 5mm pitch ball screws on all axes, so I use mm as the "native units" setting in Mach. Note that the "steps per" setting under "motor tuning" is how many steps Mach must output to advance the axis one native unit. In my case, the motor shaft is directly coupled to the screw. One revolution will move the axis 5 mm, 1/5 revolution will move the axis 1 mm. There are 2000 steps per revolution, and 400 steps in 1/5 revolution. So, my "steps per" mm = 400.
Also note that the "native units" setting is strictly used for motor tuning, and all motors have to use the same "native units". I could just have easily used inches as the native units, and the "steps per" inch would be set to 10160.
To borrow a catchphrase from a popular infomercial, "Set it and forget it".
Set your "native units" whichever way you want, inch or mm, and forget about it.
Even though I use mm for the "native units", I'm not forced to use mm in the actual gcode. I program in inches. Use G20 to set inch programming. Use G21 for metric.