When analyzing two simultaneously sampled channels, you usually want to know the differences between the two channels rather than the properties of each.
In a typical dual-channel analyzer, as shown in the following figure, the instantaneous spectrum is computed using a window function and the FFT for each channel. The averaged FFT spectrum, auto power spectrum, and cross power spectrum are computed and used in estimating the frequency response function. You also can use the coherence function to check the validity of the frequency response function.
The frequency response of a system is described by the magnitude, |H|, and phase, ∠H, at each frequency. The gain of the system is the same as its magnitude and is the ratio of the output magnitude to the input magnitude at each frequency. The phase of the system is the difference of the output phase and input phase at each frequency.