Bass boost should be at 0. Never turn it past 0 for any reason. It makes it louder by boosting the input signal, not the output. What happens is you can only boost the input signal so much. After you pass that point the music can't actually be made louder so the sound wave starts to become clipped and it will damage both your amp and your subs, not to mention your voltage will suffer terribly.
The low pass filter shouldn't be set any higher than 80-100hz. Higher frequencies will burn up your sub, simply because they aren't designed to play them (a lot of power + high frequency = little cone movement which means the sub can't cool itself very well). This will depend on what kind of music you listen to, what your door speakers are capable of playing and also personal taste.
Subsonic filter, as a rule of thumb, should be set about 5-10hz below your box tuning. This will allow it to start to kick in just as your sub would normally begin to unload because of it playing too low for what your box is designed for. Your SSF should be set at a point where you can play any song at full volume and not have the sub bottom out because of a low note.
Gain is largely misunderstood to be a volume knob. What you set your gain to is relative to the voltage coming from your headunit. Gain is basically a way of telling your amp that when your headunit is at max volume, this is the maximum it should be playing at. I use the same method to set my gains and I've never blown a sub. Take what your subs are wired to (for example 1 ohm) and multiply it by how much power your amp will put out at that given resistance. So 1 ohm x 2,000 watts = 2000. Now take the square root of 2000, which is ~44.72. This is your 'target' AC voltage that will come out of your amp's speaker terminals when playing a test tone at full volume (-3 or -5db are most common test tones, since the bass line in music will never be at 0db, you want to adjust it accordingly). If you find your subs are heating up quickly, turn down your gain slightly. If they are still overheating, your voltage may be dropping too low and the amp isn't able to make the power you assumed it would, your amp is putting out too much power for the subs, and/or your music is heavily boosted and your subs are receiving a dirty signal.