I know this post is almost a year old but... usually there's no difference, unless you pull some fancy tricks such as:
* Multiple pickups. For example, place your neck pickup on one channel and your bridge pickup on another, your middle pickup on both.
* Splitting the vibe. Add some fancy electronics to separate the tones (bass, mid, treble) within your guitar and split them between channels.
* Rotation. Put a rotary circuit in your git so that the sound "revolves" between channels (note: some people find this effect annoying and in some it can even cause nausea by affecting the inner ear).
Of course for this to work you have to have a stereo amp. If you're not running through a stereo... just go mono. Of course, you can use a stereo jack in a mono guitar. Just cut off the extra lugs or bend them out of the way.