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Okay, so I have a 2007 Civic EX w/ nav. It has the nice upgraded stereo system that hits the highs pretty flawlessly but the sub isn't quite on par with what i'm looking for. I was thinking of disconnecting it and adding in a ported sub in the trunk. I want something that gives a nice boom but doesn't take distort the sound / take over the highs. I'm still new to all the terminology when it comes to subs and stuff so bear with me. I'm just looking for suggestions right now. Anything will help. thanks!

 
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What is your budget?

I really enjoy my 8 inch Infinity Reference sub that I have. I made a custom sealed inclosure and it matches perfect. Might be good for what you want since you don't want to over power the factory system. You would only need a small amp maybe 250W.

 
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If your really into music and love hearing the bass kick, a JBL 1000watt bass with a Jensen Power 900watt amp is really a good set up. If you want less power, go with a 400-500watt amp. Always get a top rated, big company amp. As i went with a cheaper amp and it has some issues here and there. I have a 2002 honda civic lx coupe and i did have a 500watt jbl bass and 400watt amp. It was just enough. So i upgraded to the 1000watt and 900watt amp. Either one is great!

 
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I have a 2006 LX Sedan.
I replaced all of my speakers and added two subwoofers, all together it cost me about 600$
I put in all Kenwoods, replaced the door speakers with 6 in. round speakers and the rear deck speakers I replaced with 6x9's.
The door speakers and rear deck speakers are still running off of the factory deck, and then I have a Kenwood amplifier (the KAC-9105D) pushing 900 watts RMS to my two Kenwood Subwoofers in a sealed box(rated for 400 watts RMS each)

The subwoofers are loud, but I have the gain tuned pretty well to match my door and deck speakers, overall my set-up is VERY well balanced.
Here is a video before I upgraded my amp, in this video I was still using a 250 watt RMS amp(and a REALLY cheap one at that):
[YOUTUBE]http://www.youtube.com/watch?v=Aj8HUogvzb8[/YOUTUBE]
(The distortion you hear is caused by my camera's mic not being able to record the bass)

 
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No matter what brand you go for, make sure you pay attention to the RMS rating of the subwoofer(s) AND the amp, and you can pretty much ignore the peak rating.

RMS is what a piece of audio equipment will regularly put out and maintain, while peak wattage is what it can do at it's best frequency, and pushed as far as it can go.

You want to get an amp with an equal RMS rating as your sub(s), a little bit higher is ok(What I've heard is that 15% is the general rule;That is, you don't want your amp to be more than 15% more powerful than your sub(s))

This is a short video of my subwoofers with my new amp, but I played a dubstep song which is essentially all bass:
[YOUTUBE]http://www.youtube.com/watch?v=aNi_SjkugqU&list=UUG5pRsMHKWahW83U0X2qqkw& index=2[/YOUTUBE]

(The rattle at the end I have since fixed; it was my trunk vent rattling)