You could split the input feeds I suppose, but I find it more convenient to wire up all inputs--in order--since you will be feeding stereo sources in on paired cables (taped or tie wrapped, for example)
E.G:
Input 1/A Input 1/b Input 2/A Input 2/B etc
L~~R L~~R L~~R L~~R
A "Sharpie", that is, a black felt-tip permanent marker, is handy, because then you can label what goes to what right at the barrier blocks. Trust me, you will forget after a few months. Another helpful installation tip--look for those small florescent lights-the kind that plug in and you mount under a kitchen cabinet or above a sink. I mount them under the console tables to light up the wiring. Makes it easy to see what you are doing when you make changes.