If your just starting out you might want to read someone elses guide because this takes some time and big$$$. Though you can save alot by being patient and spending alot of time on ebay.

 First off, don't waste your time with wiring, do it right the first time. Use at least 4 guage power and ground wires. I recomend Monster Cable, there are others that are just as good but if you're serious use Monster Cable. Second use the same manufacturer line throughout your system. Manufacturers design there products at specific levels. Using the same brand helps eliminate Signal to noise distortion. Your amps should be rated for more than your sub-woofers, contrary to popular belief, but an over powered amp is more likely to blow your speakers. You do not want any distortion in your woofers as this will shorten there lifetime. 

You must disconnect the battery before starting, I used to believe this was just a precautionary measure, until I fried an amp. Make your first connection to your battery using either a aftermarket battery terminal or a crimp on ring terminal. Install a  fuse connector or circuit breaker not more than 12" from your battery. Use a fuse that is not rated for higher than the total of the ones in your amplifiers, the idea is that this fuse blow before your amps do. Locate a firewall access or make one by CAREFULLY drilling where there is room for one. If you drill one, install a rubber shroud to protect the wire from the sharp metal edge. Run the power wire to the inside of the vehicle. Do not hide the wire yet.

Next if you are using the factory head unit you will have to install a line drop (RCA adapter). Assuming that your installing a head unit also, it is best to use a harness adapter to your factory harness with the exception of your remote turn on wire ( usually blue or blue w/ white stripe).

Now you are ready for your audio cables (RCA's). If you're installing or  plan on expanding your system to multiple amps, use an appropriate channel cable. Normally a 3 channel cable will work (i.e. front, rear, sub). You can run multiple sub amps from eachother using their equipped pass through connections (output), or an amp processor.

Run the power wire, RCA's and remote wire (16 guage) together under the inside of the car where they will not be pinched or exposed to passenger traffic. Generally the kick plates at the door sils are the easiest.

 Now you can install the amps. Pick a place that will suit your application (i.e. underneath seats. to the back of rear seats, amp rack ect.). Make sure that there is adequate ventilation. Lay out the amps and do a general layout of the wiring. Keep in mind that some day you may get a flat tire. You'd hate to have  to remove any stereo equipment on the side of the freeway. Do not cut any wires yet, the extra length might be used later.

Once you have picked a location for the amp(s), now you need a ground connection. Use the same ground connection for all components. This will help eliminate alternator interference. I recomend installing a ground stud in the middle of the vehicle where the amps will be installed. The idea is to keep the ground wires less than 24" long. Be sure to remove any paint from the contact surface of your ground connection. 

To avoid excessive draw on your alternator (headlights dimming) use a capacitor in line with your power wire. Use a capacitor that matches your wattage to farads (i.e. 1000 watts to 1 farad, 500 watts to .5 farad). Run the power wire to the distribution block. From the distribution block to the positive terminal of the capacitor (charge the capacitor first). Make another power wire from the positive side of the capacitor to the amp. I recommend seperate capacitors for each amp. Then run the ground wire from the negative terminal of the capacitor to the ground stud.

Next connect the ground wire from the amp(s)  to the ground stud.

Now you can connect the remote wire. This wire can be connected in series to multiple amps.

Now run the Subwoofer wires. You may have to get creative depending on your channel to voice coil (vc) ratio. You can either run them in series (+Amp to +vc1 to -vc2 to +vc2 to -vc1 to amp-) or parallel (amp+ to vc1+ to vc2+, amp- to vc1- to vc2-). Make wires a little longer than needed to allow for movement.

If you are installing an amp(s) for mids and highs, run these wires now. Do not use factory speakers. Be careful when running wires to door speakers. Try to use the factory routing to avoid pinching and a possible short circuit. On some applications it's also possible to run the wires up to the head unit and connect them to the factory wires. Keep in mind that the factory wiring depending on the vehicle may run to a factory amp wich would cause problems. This is the easiest, not the best route.

Now after you have double checked your connections, you can install the fuse (with the ignition off)

Start the vehicle and power on the head unit. Start at low volume and turn all level adjustments down. Turn volume to about half way. This should be the higher end of your normal listening range. Begin tuning the highs, then mids, then bass. Once you have a rough tuning set, turn the volume up as high as you are comfortable without distortion. Retune in the same order.

If at high volume your lights dim inspite of the capacitors, then congratulations, you now have a system that requires upgrading your amperage supply. You can do this by installing higher amperage alternator and or second battery. You may even want to replace all wiring between your battery and alternator. This allows for smoother current flow from the alternator to the battery. It also adds detail to your engine Alas, your probably ready for (and in need of)  a sponsor.

Well good luck, and be careful. You start out wanting it loud and end up needing it loud.