You can make a button for instance do one function when Modifier #1=0 and one function when Modifier #1=1. In my TotalControlABCD.tci I have a couple of different examples with various complexities. In the original setup file for the Total Control there is only on example, and it is fairly simple. One clicking the button beneath the browser knob you can turn of or on the jog wheels. There is also a function for turning on the light on the adjacent button.
As you can see the field corresponds with the setting M1=1 to Modifier #1 = 1. The blue field where it says that it is suppose to be changed back to the 0 state.
Notice that the CD DJ-jog only works when M1=1.
Hopefully this will explain the basic usage of the midi modifiers.