An Electrical Engineer here.
A square wave is just lots of sine waves added together.
So when you set any Rife machine to "square wave", you are actually setting it to "lots of simultaneous sine waves".
Its kind of like adding red and blue light together to get violet.
RED + BLUE= VIOLET
The red light is still there, the yellow light is still there, but the combination looks like orange.
Similarly, if you keep adding sine waves together, the whole thing starts to look more and more like a square wave (if you choose the right sine waves).
There is a fantastic article on Wikipedia (ignore the math - scroll down to see the animation):
https://en.wikipedia.org/wiki/Square_wave
Anthony Holland used square waves when killing cancer cells in a petri dish.
In particular, Anthony used a Rife-Bare system which uses a 27.12Mhz radio-wave carrier frequency, amplitude modulated (AM) between 100kHz and 300kHz with a 50% duty cycle square wave. See www.Novobiotronics.com for his papers. Message me if you want more info.
And an extra explanation for the interested:
The Wikipedia animation shows that as you add more and more sine waves together, it starts to form a square wave (if you choose the right sine waves). The more sine waves you add together, the more the square wave starts to look like a perfectly square box (i.e. the "rise time" gets shorter). Now look at this from the opposite direction: if you directly generate a square wave with a fast rise time, you are actually generating a whole lot of simultaneous sine waves. It is this combination of different sine waves at just the right frequency that is good at killing bacteria (and cancer cells in a petri dish, as demonstrated by Anthony Holland).
Now read this paragraph again with the word "harmonics" (or "frequencies") instead of "sine waves", and it will mean the same thing.
For the interested, there is actually a mathematical formula which allows you to work out which fundamental sine waves you need to recreate any waveform. Not just square waves, but triangle waves, trapezoid waves, even a wave in the shape of the profile of the Mona Lisa. Look up "fourier series".