Here's a general guideline.
First, some definitions to help you better understand what you're setting.
GAIN - the Gain knob is the knob you use to match input voltages of the RCAs to the levels of the head unit. THIS IS NOT A VOLUME KNOB. If you go above the level of the head unit, the amp will start sending a CLIPPED signal. Clipping will bring a quick death to your subwoofer. All you do is match voltages. Anything above this point will just kill your subwoofer. It is also perfectly okay to have this level less than your head unit signal levels.
LPF - Low-Pass Filter, which is a type of Crossover or Xover. This controls what frequencies are passed through to the speaker. If you have a low pass filter, it allows all the frequencies LOWER than the filter frequency to pass through to the speaker. This is typically used for subwoofers. Higher frequencies get rolled off.
HPF - High-Pass Filter, which is a type of Crossover or Xover. This controls what frequencies are passed through to the speaker. If you have a high pass filter, it allows all the frequencies HIGHER than the filter frequency to pass through to the speaker. Higher frequencies get rolled off. You never want to use this for a subwoofer, as it is not designed to handle high frequencies and it will sound like ass. This is noramlly used for main speakers, such as the door speakers in your car.
SUBSONIC FILTER - A subsonic filter is just like a HPF. It filters out all the frequencies lower than the point. This is typically used for ported boxes, because subwoofers in ported boxes have a very hard time getting out any signal under the port tuning frequency. The subsonic filter will filter out the frequencies under the port tuning so it uses its excursion only on frequencies you can hear.
BASS BOOST - Bass boost is used to boost a certain frequency. Many high quality subwoofers don't even need this as they have a good frequency response. However, if you want to change the response curve, this is a good way to do it. However, be really careful with this. Remember DB is a RATIO, not linear. A general guideline is that for every 3dB, you will need DOUBLE the power. Therefore, if you want to boost 6dB, the amp will need to draw 4x the power compared to no boost. However, this can also be a useful tool for those with different listening preferences. Do you like a very punchy sub? Try boosting your 60hz 3-6dB and see if that helps. Do you like very low notes that make your feel like you're going to throw up? Try boosting 30hz a few dB.
PHASE - Some amps will have a phase switch. All this does is invert the signal. So instead of pushing out with a positive signal, it will pull in. In an ideal environment, this switch won't do anything. However, because car acoustics are very bad, sometimes this phase switch can help with phase cancellation.
Basic Amplifier Settings
First, put your gain all the way down, turn off bass boost. then download a set of test tones (you will probably need 20hz - 40hz, although 20hz - 100hz is highly recommended)
If you have an option for filter types (hi pass/low pass) you need to switch it to low pass. if you have a subsonic filter, turn it off or as low as possible.
First things first, put the low pass filter to about 80hz(can be eyeballed). This is a good starting point.
Next, i would set the subsonic filter if you have one and need one. Do you have a ported box? If you do there will be a big hole in the box(the port). If you have a big hole in the box, you need a subsonic filter. If your box is completely sealed off, leave the filter off or at its lowest frequency and skip the next paragraph.
If you have a port, you need to find the port tuning of the box. Turn the gain up just enough so you get some sound to hear comfortably. It does not have to be deafening. Use those test tones you just downloaded and start with the highest one (40hz). Do you get sound? Good. Go down in frequency one by one until you hit a frequency where it seems like somebody turned the volume way down. That frequency above the one that dropped in volume is your port's tuning frequency. It is usually the loudest frequency your sub can play. Now that you have found your port tuning, it's time to set the subsonic filter. Play the test tone at the port frequency. Turn the subsonic filter on. Slowly move the subsonic filter up in frequency until you hear the volume of the test tone drop. Once you hear this, back it off just a tiny bit and you're done.
Next, it's time to set the gains. Turn your headunit volume to as high as you will ever listen to it(or when the head unit starts clipping...most people use 3/4 of max volume as a general guideline). Play a test tone(any tone will work, most people use something at about 50hz). Start to slowly turn up the gain on your amp. Really take your time with this. Slowly keep notching it up until it is too loud for you to handle, the amp starts clipping, or you start bottoming out the voicecoils. You can tell when the sub is clipping when the sound of the test tone changes. If you hit this point, back off the gains a little bit and you are done. It is even easier to tell when you are bottoming out your voicecoils. If you do it gently, you'll get a slight metallic buzz coming from the sub. If you go way over what the sub can handle, you'll get almost a crackling type of sound. If you hit this point, back off the gains a bit and you are done.
A Note about Bass Boost : Listen to your system. Do you not like how it sounds? You can try using bass boost to change the response curve of your subwoofer and fine tune the system. However, if you want to use this, you will have to bring your gains back down to compensate for the extra signal you're getting at that frequency. Set the bass boost up a little bit and see if you like the quality of the changed sound better. If you do, go back and reset your gains. Using too much boost however, will make the response "unnatural." I wouldn't use too much. Also remember, that for every 3dB you boost, your amp will need to use up DOUBLE the power, so be careful not to go overboard with the bass boost and make sure the amp does not start sending a clipped signal.
Another Note about Phase: In standard installs, you will not have to worry about this too much. It's not going to make a huge difference. Go ahead and try it though. Flip the phase and see if it sounds any better? If not, just switch it back and leave it alone. The only time you would have to worry about this is if the subwoofer location causes a ton of phase cancellation.
What should the the crossover point be?
This is very subjective. Most people use 80hz as a good general reference guide for subwoofers. You can fine tune your system by adjust this point as it will help the mids and sub frequencies blend better. If you have front speakers that do not go very low and are weak in the midbass region, you could raise the xover point a little bit to help cover. However, sometimes this also causes the sub to sound "boomy." If your system sounds "boomy" feel free to try to lower the crossover point and see if it helps. However, too low and you will lose some of the "punch" of the sub which will cause it to sound a little bit "hollow." If it is sounding hollow, go ahead and try to raise the xover point and see if that helps. At this point, adjusting the crossover point is fine tuning the system to your preferences.
Should I use bass boost?
Only if you have to. This is sort of a "last resort" if you can't get the sub to sound better in other ways, such as the crossover point, or using other EQ's on your headunit or external processors.
I have a sealed box. Do I need to use the subsonic filter?
I have a ported box. My amp does not have a subsonic filter. Is my sub going to die?
Maybe. It is always better to have a subsonic filter for ported boxes. If you are not using a very high powered system, you might be able to get away with it. However, with high excursion subwoofers with alot of power, not using a subsonic filter will make the sub try very very hard to put out those low frequencies under the port tuning, when it just can't do it. If you push the gains up and make it work too hard, the sub will fail.
I hope this helps. If any of you have any more questions, I'll be glad to answer them and add to this FAQ.