Keep in mind your components will have crossovers with them 90% of the time. You'll want to run your wires that go from your head unit (normally only one set, and they are spliced into both the mids/highs) into the Xover. The Xover will 'split' the signal into highs/mids for you. If that is still misleading I can draw a diagram for you a bit later. Pretty watered down explanation but that might help clear up some confusion.
Normally the systems that run individual 'channels' from the headunit to each the highs/mids/lows are higher quality systems. Most mid level (still good) systems run one channel for each side and split it using the Xover.