The gain is the most important.
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 to prevent clipping (damage by over powering).
Here is a guide that will help you set the gain correctly http://www.box.net/shared/uchv4dbk88
You'll need a multi-meter (AC voltmeter, $15 from Radio$hack), Microsoft Excel and a way to burn an audio CD from an MP3.
If you don't have Excel, use this link http://www.box.net/shared/nkkw1dhk4g
Don't set the Bass Boost to more than +2dB
Set the phase to 0 (if applicable)
Set the LPF to just below the highest frequency response of the sub(s). Meaning if the sub has a frequency response of 20-200Hz, set the LPF to about 180Hz.
See my site for more info http://spkrbox1.spaces.live.com