I have my Kenwood KDC-X679 HU wired to my Kenwood KAC-X621 (2 channel amp). Everything sounds great but I'm not sure if my amp is set up right. My HU's manual says this:

Preout level / Load (during disc play):
5000mV/10k O (where O is the ohm symbol)

Preout impedance:
<= 80 O (where O is the ohm symbol)

I have a variable sensitivity on my amp and I set it to 5 but the bass is too low. I set it to 1 and my bass sounds fine (it can be set from .2V to 5V). Is there something I'm missing or don't know to make sure my amp is configured the right way? There's also two small graphs on the amp that says HPF Operation and LPF Operation with some lines on it, what is that used for?

Usually the technical data for the preout level and impedance isn’t needed. You just tune by ear, since you're going to be listening to it. As long as you hooked up everything correctly you shouldn’t run into any problems that will damage your hardware.

The LPF and HPF on the other hand are rather important. LPF = Low Pass Filter and HPF = High Pass Filter. If you are running a sub with the amp you definitely want to put it on LPF. There should be a switch on the amp that has LPF, HPF, and No Filter. If you don’t change that, your sub will be getting high frequencies and there is the possibility you will crack your sub. If you are running normal speakers with the amp than you don’t need a filter and if you have an amp running your speakers and a different amp running a sub than you would set the one with the speakers on HPF so the speakers only get high frequencies and the low frequencies are sent to the sub.

Other than that, just adjust the amp to your liking. There is no strict guideline as to what you have to set it at cause most of them are just analog knobs. That is unless you have an Alpine or something to that affect.

I have LPF on and the cutoff frequency to 50Hz. My bass sounds good but on some songs (especially Young Buck - Ride wit me), the sub sounds weird, like it's being cut off but when I had my stock HU, it sounded fine. Any ideas?

Um, what are the models/specs for the sub and amp. You might be pushing the sub to hard and sometimes when subs distort they sound like they get cut off or vice versa. You might want to try turning down the gain/bass boost on the amp. It might be a power issue as well so either the model #'s or specs are needed.

Amp: Kenwood KAC-X621
Sub: Pioneer W304DVC (I think)

Sub specs:
300w RMS / 600w total sub, dual 4-ohm sub (wired in parallel to make a 2ohm load on amp)

Amp specs:
300watts x 2 @ 2ohms (or 600x1 @ 4ohms bridged)

My setup is wired in regular mode, not bridged so I'm pushing 300 watts to my sub so it should be right. I just listened to it and it sounds good from the driver/passenger seat but when I stand infront of the sub, it sounds kind of distorted. I want to upgrade the sub to a Rockford Fosgate T112D2 ( http://www.rockfordfosgate.com/products/ez2rockford/ModelInfo/ModelInfo.asp?ItemKey=10065578&CategoryDesc=Power%20Subwoofers , dual 2ohm sub which I would wire in series for a 4ohm load at the amp and push 600watts to the sub)

Try bumping the LPF on the sub up to 60 ish, maybe 80.

Right now you're only getting the really low bass stuff....and a lot of the stuff you'd normally hear is taken out by the x-over.

Here's how I have tuned systems for the 13 years I have been doing them.

Turn your radio up about 7/8 of max volume and adjust the gain until the ouput is slightly distorted, then back off slightly. You can get a feel for max clean output.
The reason that you don't wanna turn your radio all the way up is because both RCA level outputa and speaker level outputs will distort at max volume, a.k.a. clipping.

I have LPF on and the cutoff frequency to 50Hz. My bass sounds good but on some songs (especially Young Buck - Ride wit me), the sub sounds weird, like it's being cut off but when I had my stock HU, it sounded fine. Any ideas?

2 things you should know.

Alot of new rap- especially southern, is recorded like complete trash. They dont use clean bass notes, always distorted trash so tuning to an artist on Cash money records or the likes is the worst idea you could do.

setting the crossover at 50hz is probably too low...

Lots of GREAT info in this thread.
I really can't add anything to whats already been said!
(I'm floored by that really).

Re-read everything said in here and pay attention. Good stuff!