I am going to jump out on a limb here and assume that you are talking about running a program like sonar where you can choose on the input side.
Remember that mono is one, and stereo is two. So if you are recording drums with two mics, one mono mic on left and one mono mic on right, when you mix you can choose what it sounds like by PANNING the channels.
IE: If you choose to have both the left mono signal and the right mono signal, play back in the middle, then you will have a mono mix, if you PAN the right mono mic to the right and the left mono mic to the left, then you have a stereo mix.
I am not sure if I got at your question or not.
Give some more info.