I suck at EQ's help me out.

[BR3W CITY]

Audio settings baffle me after the basic stuff, so help me out here.
2005 Yukon,factory Bose system (oe sub not used). Added a Pioneer 4200NEX, and a 12" L7 with a Kicker 600w amp.

I have EQ and audio settings on the deck (graphic EQ, etc), and a set of knobs on the amp itself. People have said use one or the other, not both... but they don't have the same settings?

I've seen other posts saying to set the amp "neutral" or "flat", but what is flat in terms of my amp? Its not like the settings are all 0-10.

I'll post a pic of the amp settings when i can. My system sound alright, but the sub is very boomy on some tracks, and yet lacks volume on others. I've played with settings before but I don't think I'm helping.