The deck's preamp output is a selectable rear or sub output. The only difference is when its on sub mode it simply enables a low pass filter. However this is not needed if your amp for your subs has a low pass filter on it. Using the adjustments on your sub amp wont affect your other speakers. I hope that makes sense lol

The best idea would be to get a deck with 3 sets of preamp outputs such as this Kenwood Excelon for $169.99 http://www.crutchfield.com/p_113KDCX...-KDC-X592.html