What does it mean to have a 2-channel interface? like the Alesis io2? Does it mean that it send two totally different signals to the PC? Or does it simply mean that it uses two inputs to form one recording.

Im so confuzed.
you can use it for both. you can record two separate instruments simultaneously on two different tracks or DI you guitar and mic the amp and mix the two sounds. Also I have a spider jam amp that has stereo out so I can plug the left in one channel the right in the other and record it as a stereo track in my DAW. either way you will always have 2 separate recordings.