Last question first: Room is coupled with Echo because they are designed to give you the impression of being in a larger room. Basically it is a reverb function.

As for your first question, let's take them in order in which you should adjust them:
DSP Equalizer - Use this to get a flat (or otherwise if you prefer) frequency response in the car. Generally these are set using test tones.
Amp Crossover / low pass filter - Needs to be set in combination with the DSP amplifier. This is not a volume control it is an adjustment to determine what frequencies the subwoofer reproduces. This is a "set it and forget it" adjustment that is appropriately set when the subwoofer is picking up where the next speaker leaves off.
Bass / Treble - Use this to adjust for individual tracks / sources. Should be used in combination with
MP3 Equalizer - May be helpful to set this up to provide a similar signal to your FM input.

You have an interesting issue - typically FM has the lowest amount of bass relative to CD, Aux, or Ipod...


Doug