The last 'toad' I had was a Scion XB (motorhome tow-car). I installed a unit as I've pictured below, or one that looked just like it, under the passenger seat. Although it took most of the toe room for the right side back seat, it was otherwise virtually hidden. We had the car for about 3 years and it worked out just great. Never bothered the passenger either unless you cranked it full. LOL.
A powered sub either connects to a sub outlet from the HU or, you wire speaker leads though it and it takes the signal and amps the base. They are fully adjustable so that you can set where it kicks in in hertz, it's strength, and volume. Once setup it's a very nice augment to the overall sound experience. The radios that come with these cars are not all that great, so they definitely benefit from a powered sub.
It's a power hog so it needs a heavy duty lead direct from the battery with a large inline fuse. You just run a lead in thru the firewall. There is another lead on the HU that is a signal switch to power up the sub. That way it only turns on when you turn on the radio.
I was hoping to hear from someone that had installed the upgrade speakers with the 'A' radio, tell us if they're worth it or not.
IIRC this is the e-tailer I got it from, they have several styles: http://www.onlinecarstereo.com/Help/HelpContact.aspx