Ah, I see you've been listening to NAFSPARK over at the icixsound boards.
http://www.icixsound.com/vb/showthread. ... ge=2&pp=10
Technically he's right -- setting your gains with the EQ set the way you like may sometimes clip the output of the HU or the amplifier itself. But don't let anyone tech-talk you into getting too anal about it. Busting out an oscilloscope isn't going to make your system sound any better than one done by a careful ear.
Edit: ah, cntrylvr79 beat me to it. Like he said, turn down the amp, balance out distortion by ear, then adjust the amp. It's more of an art than a science.
Yes, I have been listening, I try to be a quick study. 
I have almost all the equipment from that schematic sitting in my home, the D3 is already installed. I have some sound deadening done as well, but not all. No time lately, with son being sick and myself and wife it's been difficult to set aside time.
I'm waiting for the sub enclosure to get in, then the rest gets installed, I'm just trying to do it all "right". Wait is killing me though.
I'm trying to get a clean signal from my HU, I don't want my HU distorting. I'm trying to avoid distorting anywhere down the line actually. I'd prefer to be safe and have it all be clean all the time, I understand not all things are recorded at the same level, etc. Nonetheless I'd prefer not to push beyond the limits of my equipment and possibly damage something. Even setting everything within these safe limits using "geek scientific" methods I figure the volume levels should be loud enough to keep me grinning happily. 
cntrylvr, don't worry about me in that sense, rap and/or hip hop will likely never "grace" my sound system if I'm alive, definitely not my thing. House music for me, the occasional trance, techno, etc.
Thanks for everyone's input thus far.
When I finally get around to it I'll post back with my results in case someone else down the road is doing a sound system and searches like I did. lol