We had a 21 Stealth and the system sounded great for the money we had into it. We had two JL W0 12" subs, one under the dash on each side. We ran them with a JL 500/1 digital sub amp. We also ran 2 pairs of 6 1/2" JL component speakers and 2 pairs of 6 x 9's. I powered the mids with the JL 6 channel amp. 2 of the 6 x9's were in pods under the hatch to throw the sound towards the beach when we were nosed in. I ran the interior speakers on the front fade and the hatch speakers as the "rear" fade so we could send power to the speakers as needed. No need to crank the interior speakers when we were on the beach.
The JL amps never over heated and they didn't drain a ton of power from my two batteries.
I am currently running the new Alpine PDX amps and they are great. Small size and they don't use hardly any power yet put out a loud clear signal. Maybe run the PDX 450.1 for your interior speakers and then run the subs with the cheaper JL 500/1.
As for matching sub to amps....always get the subs larger than your amp that way you don't blow the subs with too much power, but just as important...make sure to match the ohm rating of the amp. Most good digital sub amps are stable to 2 ohms. So get two 12" subs at 4 ohms and wire them parrallel so the amp see's two ohms.
I have run a large single 12" sub in the past but I think it's easier to make good sounding base with two decent 12's instead of one super powerful 12.
Just my $.02,
Chris