I personally prefer a properly designed ported box with a suitably chosen driver. I like the sound better, generally has more audible output, and driver excursion is GREATLY reduced at lower frequencies (the sound is generated mostly by the port rather than driver excursion at the tuning frequency). However, it is VITAL to have a subsonic filter when using a ported box!! Below the port frequency, the port is just a hole in a box and doesn't limit driver movement at all. That, and output drops precipitously (-24db/octave IIRC) below port tuning frequency. Have to use the right size port too or you'll get "chuffing" noises. You can use dual ports or a single larger port, but keep in mind the larger in diameter, the longer the port needs to be for a given frequency.
A sealed box can go deeper and tends to have a flatter response curve, but it takes 4x more excursion (and more power) for each drop in octave to get the same output.
But, you can't just toss a driver in any old box you happen to have. The driver must be suited for ported or sealed or free-air or band-pass, and the designer must use the proper formulas based on the driver's Theille-Small parameters to design the proper box dimensions.
The actual geometry of the box makes a difference too. A cube box will tend to be boomy. The reason most boxes have different size dimensions is to reduce standing-waves from multiplying inside the box.
Then, you have to use proper materials. Whenever I built an enclosure, I use no less than real 3/4" thick MDF dado'd and glued into place. Then, fiberglass all the internal seams. I usually used a double layer for where the driver mounts to allow a flush driver installation. Then, use the right amount of poly-fill (makes the box seem acoustically larger). Don't be surprised to have a heavy box; my boxes (which were usually for a single 10" or 12" driver) weighed around 60-70lb by itself (without speaker).
Wiring is not too tough if you take your time. Head unit wiring is MUCH easier if you just go get a wiring kit for your vehicle. That way you can just wire it all up outside the vehicle - the wiring kit color-code is the same as most head-unit color-code, so it's easy. Vehicles use all sorts of wire colors and I will say to properly identify each speaker and the proper
speaker polarity can be a pain (isn't too bad if you know a few tricks though). Just get the kit and save yourself the headache. If a previous owner did the dumb thing and cut off the stock vehicle harness, you can get color codes from here:
http://www.the12volt.com/
As far as amplifiers are concerned, size/wattage depends on the person. If you're a basshead, then no amp is big enough. But, if you're looking for decent sound, I generally go with 2-3x the power of the regular speakers. So, if your deck puts out 20w x 4 (rms, not "peak" - gotta read the specs carefully), I'd go with between 160w-240w rms power for the sub amp. Use a crossover on the main speakers to limit the bass (either use the "active" HPF in the deck, or use a "passive" 200uF non-polarized electrolytic cap in series with each speaker), and set the amp's LPF for around 100Hz or lower (the higher the LPF value, the more voices you'll hear out of the sub and you don't want that).
For total amplifier power of 500w rms or less, 8GA power wire is adequate. Up to 1000w, use 4GA. Higher than that and you'd better know what you're doing.
For subwoofer power, get a sub that will handle the value of the amplifier. It won't do any good to get a 1000w sub and hook it to a 100w amp - subs that large will likely be less sensitive and won't sound good with low power. It's also bad to run a 1000w amp on a 100w sub (obviously). However, if you do it right, they don't have to match exactly. I ran a 300w Alpine TypeR sub for several years on a 600w rms PPI amp (yeah, old school stuff) with no issues whatsoever. You just have to run it clean - no amp clipping and no mechanical distortion.
All right, that's car audio 101 in a tiny nutshell. Probably more than you wanted to know, but there ya go.