Subs and Pioneer cd player

I have the mach460 speakers and amps in my car but replaced the head unit with a pioneer p6600. I recently purchased two 10" MTX thunder 8000 subs (4ohm DVC) and an MTX Thunder942 amp. The amp says it gets most power at 4ohm bridged. I wired the speakers together with a 4ohm load total. Couple questions. The only way I get any sub control (whether I can turn it on/off) is if I turn the cd player off and go into function and change the SW setting from FULL to S/W. When its on full, the sub does barely anything. But what seems to happen is that my rear speakers are acting as subs when I do that so I cant crank anything up too high without them distorting. The amp also doesn't hardly do anything unless I crank the gains to max, and the eq to max and everything.
I would really appreciate your help, setting up my cd player and amp. I would like it if you could explain what the 2n,1n,1w,2w setting are when I press and hold 'audio'. There are also things like 40-160, 200-1000, and 2.3-12.5k.

Thanks alot. I'd really appreciate your help.

Feel free to IM me at BoostedStang302

TTT
Anyone know of any good sites to learn a bunch about this?? I'd like to get more information about this. Anyone have any ideas why my sub doesn't hit very hard unless I crank the volume up pretty loud?