If we get the sound from microphone with two channels, to calculate the frequency spectrum we:
I assume your two-channel microphone has inputs that are physically separate - typically, opposite sides of a lecture hall or theater. In this case, the Fourier transform of each channel shows you the frequency content at the physical location of that channel's input - you can't just average them or add them together and get any meaningful result.
If you're trying to get the spectrum at the midpoint between the channel inputs, averaging might make sense, but anything else would require some big assumptions (reflection not a factor, etc) and interpolation.
Any meaningful analysis of this data is going to have to take into account the physical geometry of the space where the sound is sampled. Clarify what you're looking for.
Oh, and tag your posts as homework.