it doesnt really make sense, but i use the crossover settings on both the head unit and the amp, it seems to work better,it shouldnt but it does.
gain is the amount in which the amp amplifies the signal it is given, while it acts as a "volume" knob, it really isnt. you will notice it is labeled 6v to .2v. it should be set to match the voltage of the preouts of your head unit. if you go higher you get clipping. most head units are either 2 or 4 volt preouts so it should probably be turned a little less that top center.
LPF is low pass filter, it cuts out frequencies above what you have it set at. you can hear 20 to 20000 hertz, a subwoofer should be playing as low as it can go up to somewhere in the 100's depending on the sub. so if your sub can go to lets say 25hz and you set the LPF to 120, then the sub will only play frequencies between 25-120. this is used to keep higher pitches like voices coming out of your subs.
HPF or high pass filter is the exact opposite, it is used to keep low bass from going to your interior speakers, lets say you have 4" speakers up front, they have no business trying to play frequencies near the 20hz mark. this is where im a little lost though, so im gonna pull a number out of air, i think a 4" shouldnt play frequencies under 500hz. so if you set the knob at 500hz then the speaker would play the sounds between 500-20000 or as high as it could go.
those x1 - x10 switches next to them just change those knobs from 50hz - 500hz to 500hz - 5000hz, most of your full range speakers can play 500hz pretty well except tweeters, so id say leave it on 1x.
i wouldnt say stay away from bass boost entirely, but do use it sparingly, some of your tougher subs like kicker, and surprisingly sony can take a beating and would probably be fine.
subsonic im not really clear on, but from what ive read, its just kinda like a high pass filter, but for a very low and narrow band of frequencies, so lets say you set your LPF as 120hz, so your sub is limited to 120 and down, and the lower end is only limited by what the sub can and cant actually produce. sub sonic would actually put a cap on the lower end to like the hpf, but only to somewhere in the neighborhood of 20-30 hz, the idea is if the sub cant play down to 20 hz then sending the signal to and and making it try to could damage it. ive never felt a reason to turn it on, so id just have it set as low as it can go. but if your using 8" subs you may want to set it up to what the lower freq the subs are rated for.
hope this helps