Benchtop Frequency Counter - what does the AC specification mean?
Freq range: DC couple 0.01-100Hz; Can't use DC coupling. AC couple 100Hz-50MHz. AC coupling OK.
Sensitivity: "DC" 0.01-1Hz = 500m Vp-p, 1-100Hz = 80m Vrms, "AC" 100Hz - 50mHz = 80m Vrms. Your signal exceeds minimum sensitivity so the counter will detect it be we need to make sure you 60 V signal won't damage it.
Input impedance: 1 M? [Looks as though whoever typed it couldn't figure out how to insert an Ω.] 1 MΩ is typical for an oscilloscope and should be suitable for most measurements. 


Channel B (50MHz - 2.4GHz). Channel B doesn't appear suitable.
Freq: 50MHz - 2.4GHz
Sensitivity: 50MHz-1.2GHz = 80m Vrms, 1.2-2.4GHz > 80m Vrms
Coupling: AC only.


  Need to accurately measure frequency of an AC square wave from the 1 Hz to 5.5 kHz range, 2 - 60 V peak to peak.



Use channel A.
There is no maximum voltage listed for channel A so it would be wise to use a 10:1 probe or resistive divider. This would take the voltage down to 6 V p-p which should be fine.