Im guessing your running the speakers from the CD player, and the amp is for the subs.
lets take it step by step, i'll try to keep it simple, first the eq's
bass eq- id guess there are some numbers like 40, 55, 60 etc, these are frequencies, low Hz, set the numbers to your liking while listening, if your subs are in a ported box, set the eq higher at your port tuning freq.
LP crossover freq- This is for your subwoofers typically its a knob from 30/50-100/300 turn it to your liking as well, i suggest about 100hz to start out.
HP crossover freq- dont use this for subwoofers unless it goes down to about 10-30 hz, then you can use it to block out ultra sonic frequencies, stuff you cant hear, that muddies up the music.
keep the gain settings at the factory setting, and adjust as you turn up the volume on the CD player (head unit),
at about 3/4 volume of your head unit turn the gain up till there is enough bass for you, or distortion occurs, this is not a volume knob!!!!
good luck, hopefully i didn't miss anything!