The purpose of the gain is to match the signal volts RMS coming from the source (CD player, etc.) to the input of the amp for correct power matching and to prevent clipping (damage by over powering).
Here is a guide that will help you set the gain correctly
http://www.box.net/shared/uchv4dbk88You'll need a multi-meter (AC voltmeter, $15 from Radio$hack), Microsoft Excel and a way to burn an audio CD from an MP3 (test tone included).
If you don't have Excel, You can downlaod OpenOffice by Java (SunMicro Systems) for free to read spweadsheets (and you thought spreadsheets were for business).
Set the LPF to just below the highest range of the frequency response of the subs. Meaning if the frequency response of the sub is 20-200Hz, set the LPF to about 180Hz
OR
set the LPF to where the other speakers start off. example, if the speakers start at 150Hz, set the LPF to about 160Hz. This overlap (or crossover - where the term comes from) is the ideal setting.
Set the subsonic (infrasonic) filter to about the same as the lowest setting in the range of the frequency repsonse of the subs. Meaning about 20Hz if that's the lowest in the range (20 -200Hz as above, if applicable).
Don't set the Bass Boost above +2dB (if applicable).
Set the phase to 0 (if applicable).
See my site for more info
http://spkrbox1.spaces.live.com