well, higher wattage isnt always better. Speakers have sensitivty ratings, the higher the sensitivity, the less power is needed to achieve the same volume as those with a lower rating, every 3 decibels higher in sensitivity(spl) half the power is require to achieve the same volume as something with 3db less in sensitivity.
now that that is dispelled, when you purchase an amp it will come with a gain knob, atleast any good amp will. This knob controls how much signal is translated into volume. The goal of this knob is to enable you to have everything in your system peak at the same time so things dont start to distort at different volumes. This is also known as calibrating it. Now, you dont have to do this, you can make it so yours subs peak out at half the volume of your speakers, why, i dont know why you would want to. However, if you find that you have too much bass with it calibrated, you can reduce the gain so the subs dont get as loud when you increase volume. This isnt something you would want to change everytime your wife rides in the car with you since its on the amp. Depending on what subwoofer features your headunit has, you can usually adjust the bass from that, but then again, this is all headunit dependent.
You would be surprised how much bass is really needed to shake your mirrors, not much at all. I had 1000 watts in my old car and i loved it, i have changed a bit, i prefer less bass down and a more accurate system overall, but there are definitly times where i want that 1000 watts bumping.
500-1000 bux will get you a nice system if you purchase stuff on the internet. Space seems to a bit of concern for you so i dont think 15's would be a good option. You can purchase 8's 10's or 12's, 12's will be the most of the time for producing the lower tones. If you want, you can look into slimline woofers, jl has one as well as pioneer and a couple of companies, i just dont know them offhand.
I like sealed boxes because they take up less room than ported boxes. Sealed boxes are able to maintain a fuller freqency range then ported because the port tubes are tuned to certain frequencies, they are also louder than sealed boxes because less power is needed for compression. However, ported boxes tend to be more sloppy than sealed boxes, this usually goes for car audio and not home audio, car audio just doesnt have that type of refinement in enclosures since everyone has a different application.
For your price point, you can look at alpines, jl's, rockford fosgates, soundsplinter, as well as a bunch of other brands. Now keep in mind, there isnt necessarily a benefit of 2 subs over 1, you can have 1 sub beat out 3 subs depending on what kind it is. If you want to, go to
http://www.woofersetc.com and peak at the brands that are on there to see what products are offered. Ask questions along the way, they really have a pretty wide selection of stuff. I have never bought from there nor do i think i would, i just like them since they have a good selection.
Amp wise, i like alpine, jl, rockford fosgate, there are many other good brands as well, everyone has a preference and it is NOT worth it to skimp on your amp. Alot of brands are overrated as in they say it produces 4000 watts peak, if you look at their numbers, it doesnt produce anywhere near that in reality. Us Amps are supposed to be good as well and MB Quart. Just peek around.