Here is a link of some pics of mine.
http://www.geocities.com/snaglpus00/
Mine is a lot more then what you are looking for - check my sig, but might give you an idea on how to put your sub in the tirewell. There are other write ups on how to do this. Its the best sounding in my opinion but you lose your spare.
Next is how much are you willing to spend on it? 1K, 2K, 5K?
Do you want Loudness or Sound Quality?
Are you willing to add some extra weight (box, sub, dynomat) If so how much?
Want a GPS/Sat Radio setup?
Ready to replace that stock battery with a Optima?
Do you want to run 2 amps (sub and highs) or a 5 channel single amp?
If you are really a newbie and don't understand / know much about stereos I suggest finding a friend that knows about it or getting some stuff professionally done. I ran all the wires and did more the speaker installs and let a shop do the rest like building the custom box.
What ever you do, scrap the WHOLE system and build a new one. Remove the amps along with the front and rear speakers. The stock speakers are made to run on a 2ohm load and after market amps are normally 4ohm. (ohm is resistance, the higher the number the more resistance but its best to match them all up unless you know what you are doing - won't get into trying to teach bridging and all here)
Stick with High Quality Products, even cables should be of good quality.
List of what you might need for a good install.
Quality HU (Apline, Clarion, etc - Try to find one with 4v Pre-Amp outputs)
Quality speakers (Polk, Kicker, Inifinity, etc)
GOOD SUB - JL need I say more!
CUSTOM BOX!!! for the sub you buy! Box should be built to the sub's specs.
Amps (I am a old school Rockford fan, but just get a good amp not a cheapo, bad amps lead to problems like blown speakers and over heating)
New GOOD battery - Optima preferred.
0-4Ga Power Wire
ANL fuse or Circuit breaker for power wire
Fused Distribution block.
More wire to go from the distribution block to the amps.
RCA cables
Sound Deadening (put some behind all the speakers doors and rear and the sub)
The price can really add up, but its better to do it right once then be fixing problems and replacing parts for the years to come. Trust me I blew my Rockford HX2 sub twice before buying a JLW6 so I paid for 3 Subs instead of just 1 to start with. Not to mention I bought a cheap fuse distribution box that melted on me with the first sound off. In Car Audio you get what you pay for!
~K