You did not pay attention (or the person installing it didn't) to the configuration of the factory amplifier.
The mod to make it all a four channel system is pretty simple:

• Add four wires from the new head to the amp
• Cut jumpers at the amp and wire the new leads from the head to the amp's third and fourth channels.
• Set up EQ and fader controls in the new head

Look here:
https://www.crossfireforum.org/forum...-channels.html