Is this a four channel amp? I'm no expert, but basically, if it's a 4 channel, you would use the front channel output off the head unit to feed one side of the amp, which in turn feeds your front stage, and then use the rear channel from the head unit to feed the other side of the amp, and that side feeds your subs. You can then use your fader somewhat as a sub level control.
That's why it's great if you can afford an after market head unit, because a decent unit typically has a separate sub level control, and many units will also have sub frequency control.