You will want to turn the bass on the deck down, yes... what you do, turn the bass all the way down, and then find your "listening level". Keep the volume there, and slowly turn the bass up again untill you hear distortion, then turn the bass back down to eliminate the distortion. Then, with everything on the deck set, start dialing in the sub bass, get it to where it sounds good without distortion, and you're all set.
Your bass will be noticably louder and fuller than just the stock speakers, even with the bass turned down on the deck. You'll also be able to achieve louder listening levels, because the main speakers wont be producing the bass, instead your sub, which is made to produce the low frequencies will handle it.