This stereo does not have a subwoofer output, therefore you wont be able to control your subwoofer through this stereo. You can run the speakers wires to your active subwoofer and control the settings of the subwoofer through the subwoofers amplifier's settings. Other than that, your options are limited when it comes subwoofers. The only settings you can control from the stereo are bass and treble.
Are you trying to use this stereo to run your subwoofers. If so, you need a "RCA Y-adapter" to connect to one of the AUX connections. (That's if your connection is RCA.) If not, then you will need some type of converter to convert your speaker wires to RCA connections. Google "speaker wire to rca converter" and look at IMAGES, this will give you an idea.
I hope this helps, if not, then apologize in advance.