There will likely be differences of opinion on this but this is mine.
I'm assuming the rest of your system is OEM since you made no mention of it. If you are trying to get the purest sound possible, begin by turning off all the sound processing. You always want to start from a flat output and then adjust the system to fit the environment and your taste. If you've already been listening to the stereo for a while, turn it off for at least 5 minutes to allow your brain to forget what you were hearing.
First turn the subs off. You have to get the sound levels of the components where you want them and then adjust the subs to complement them. Adjust the bass and treble or if you must turn the SSP on where you are happy with it. Once you are happy with the comps turn the subs back on. Begin by roughly setting the gain so the subs complement the level of the comps. Then adjust the crossover. Normally it will be at 120 Hz or less. The lower you go the smaller the frequency range they'll have to play which will make them more efficient and therefore louder and cleaner. However, if you go too low you'll have a hole in the overall spectrum of sound.
Once you have the sound right it's time to set the gains. Since everything else is playing from the radio all you have to do is adjust the gains so the sub volume complements the components. Subs are reinforcement. The comps are supposed to be producing most of the music.
I'm sure someone will post that you have to turn the volume up until the system distorts then back it down a touch. Then do the same with the sub gains. That method is meant to set your comp levels when you have separate amps. It was not intended to balance the sound of the subs to the rest of the system. Your subs can overpower your comps easily. If you follow that method to set the gains, you'll have nothing but bass.