Firstly check what type of amplifier it is actually before tuning a car amplifier.. whether it is a stereo amplifier or mono amplifier as they both have different type of tuning adjustment knobs and they work differently. The main control of an amplifier which can cause damage if not controlled carefully is the gain control on both the amplifiers. You have to know the main function of the controls given in the amplifier so that you will be knowing what you are doing while tuning the amplifier.
Main functions of the knobs are:
Gain: It is for controlling the voltage coming out of the head unit of the car. If the output voltage of car radio is 4 Volts then the amplifier gain should be set according to 4 volts. Going beyond the limit of radio can produce noise in the sound or can clipping/distortion. It works like volume control but does not be treated like volume as it can cause damage to amplifier if it gets beyond clipping. Gain is the main tuning of a car amplifier.
LPF: It is usually found in the mono amplifiers and some stereo amplifiers as well. The main function of LPF is to limit the higher frequencies for not coming into the set level of the LPF of amplifier. The subwoofers cannot play higher frequencies so the LPF is set to 80Hz so that the frequencies above 80Hz should not arrive to the subwoofers.
HPF: It is only found in the stereo amplifiers and is very helpful function for the speakers to perform. Its function is to limit the lower frequencies and not let them come in the speakers as the speakers are not designed to produce lower frequencies like subwoofers. The usual frequency at which HPF is set as 80Hz to 120Hz according to the size and make of the speaker and your taste as well. Too much high HPF level can result in less vocal/mid in the music.
Subsonic: It is only found in the mono amplifiers. It is used to create a band between the LPF and the subsonic so that the subwoofer does not go too low at which it cannot handle the frequency. Subsonic helps to set a limit of subwoofer frequency at which it does not go beyond that level and not play the frequency below the subsonic level. The subsonic is set to the subwoofer enclosure tuning frequency so that the band is created between the enclosure tuning frequency and the LPF frequency. The subsonic is considered to be the main tuning of a car amplifier as it prevents the subwoofer from damaging its voice coil by playing lower frequencies which it is not designed to play.
Bass Boost: It is found in mono amplifiers and is used to boost the decibels of the bass boost frequency. It works parallel to the bass boost frequency. You have to set the bass boost frequency first and whatever the frequency you choose the bass boost will boost it to super loud and you will feel that the bass is insane because of using bass boost feature. But this comes at a cost which is bass boost creates a peak in the frequencies so whenever you will play music you will feel insane loud bass but only that frequency itself can be heard and other frequency will not be able to identified as they will get behind the peak of frequency you set and it will roll off to left and right in overall spectrum. Many amplifier manufacturers write on their amplifiers that not needed on the bass boost part of amplifier.
Bass boost frequency: It is found in the mono amplifiers and it works with the bass boost feature only. It functions like whatever the frequency it will be set at the bass boost will increase its decibels and creates a huge peak. So the frequency becomes louder as it is being boosted artificially. It will dissolve other frequencies lower than the bass boost frequency to be lost in the music. Suppose you set bass boost frequency to 60Hz then you will not be able to feel 40Hz or 80Hz in the music. This feature make bass loud but make the overall imbalance in music. It should not be used if you set your gains properly.
Phase Shift: It is a function which changes the phase of the subwoofer 180 degree around. Like sometimes your speakers and subwoofers are connected in same polarity then you might face phase issues so to correct them either you switch the polarity of subwoofer or you can change the phase of subwoofer 180 degree so that speakers and subwoofer does not cancel each other.
The desired frequency of LPF is 80Hz
The desired frequency of HPF is 80Hz
How to start tuning the amplifier
This is the most crucial part of tuning a car amplifier that you will have start from the head unit. Set everything to 0 and off the features like bass boost and equalizer to flat and now you will have to realise if you wanna use any features like bass boost or equalizer setting you have to do it now as if you set the setting on amplifier and then you change the setting on head unit the things can go very wrong. So set the equalizer setting to your desired taste and start with tuning the speaker amplifier first. firstly turn up the volume of the head unit until it is 1/3 of the full volume and not clipping. Then slowly increase the gain of the amplifier till where the sound does not seem to be changing as the distortion arrives if gain is over adjusted. Then slowly set the HPF of the speakers to 80Hz. Make sure the speakers are playing good enough with your gain adjustment as you can over push speakers while playing on amplifier.
Then come to mono amplifier and set the HPF at 80Hz and the subsonic to your enclosure tuning frequency or the subwoofer Fz frequency. After that come to the gain adjustment but before that if you using bass control on mono amplifier turn it all the way up so that you cannot accidentally open it full one day and thing will go boom! So turn it all the way up so that you can reduce the bass but not accidentally open it more. and then set the gain to the level where it is not clipping and sound is not getting changed in any case. Do not use bass boost frequency and bass boost feature if it is not necessary for you as it is not recommended by most of the manufacturers as well. But if you wanna use it you can set the frequency of your choice and boost it to the level you are happy with. make sure it is not clipping at that level. Over limit use of bass boost will fry the subwoofer coil in seconds and boom! Be careful.
You can read types of Head Units for Car Audio to learn more about car audio.