amp and hu config

Do you want more bass? You can use those subs with the amp. Simply wire one woofer to each channel. Set your headunits subwoofer level to 0 (to start). Now make sure the gain on your amp is turned all the way down (counter clockwise). Now turn the headunit's volume up to where you like to listen to it. Next slowly turn the gain up (clockwise) until you begin hearing distortion. After you hear some distortion, turn the gain back down alittle until the distortion goes away. Now your amp is set. From then on, you can simply increase the headunit's SW level, but chances are you will hear distortion so keep it at 0. Then listen to your subs and see if you like them. If not, then your amp isnt powerful enough. Now onto your frequency knob. Make sure you have the crossover to low pass filter. Next turn the frequency knob to about 200 to start. If you have it at 40, (which by what you have said) then you hardly have any mid to high bass going to your subs. Start it at 200. Listen to it and if you hear alittle treble going through your subs, then slowly turn it down until you only hear bass. That is basically what your amp can put out without including EQ's and external crossovers.

you will have to run those subs stereo off of that amp.  if you bridge em, you will end up with a 2, or an 8 ohm load.  2 is too much for that amp bridged, 8 may be ok, but won't necessarily push the amp. stereo 4 ohms will probably give you pretty good sq, and should be ok for those subs, you'll have to try it out. 

what kind of box- to mfgrs specs? also, how is it placed?  i find that most boxes sound best (to me) firing back at the trunk, or down. 

also, assuming all power wire, connections etc. are ample for your load(?)

frequency knob, i believe, is your crossover on the amp.  if that is set at 40, then it should make no difference in sound if you change the crossover setting on the deck to 100- the subs will still only see 40 hz and below.  i usually start my adjustments on low pass crossover at 80-100hz.  that is usually a good starting point for twelves.

yeah, if i was in your situation, i would opt for a mono-block amp and run at 2-ohms.  if you can find/ afford a two channel that is stable into 2ohm mono (will probably be listed as "stable to 1ohm stereo"), then that will suit your purpose also. 

otherwise, you are probably going to need an 800-1000 watt amp to get them to push at 4 ohm stereo-but the sound quality will be alittle better.  just keep in mind that a lot of amps out there are overrated.  just because you see a 2000 watt amp on e-bay for $100, doesn't mean it will sound any better than a $400 amp that is only stated to have 500 watts.  a lot of companies are fudging the stats to look better.