Not used "FreqCount" library myself, so maybe someone else can advise about this library. The comparator input signal goes in on Pin 18 and the sq wave output comes out on Pin 2 (and the code would go into Setup).
If you have a T4 at hand and a scope to see the waveforms, have an experiment to see just the comparator in action.
Edit. As a Radio Ham myself, I should emphasize that high power R.F. signals have a nasty habit of invading/inducing wiring, so can do a lot of damage. If you are thinking of building your own Freq Counter make sure you experiment with a low power sig generator first. And when it comes to using in a "harsh" environment, your screening/earthing/isolating will have to be first class.