IMO, go to a shop, take a listen to what they have and talk to their installers. Tell them what you want and listen to their ideas. Base your decisions off of what you want, while taking some input from them. Since you asked about this, I honestly wouldn't install it yourself. Get a reputable shop to do it and have them custom build a box to match the subs you choose.
Your budget will have a huge impact on what you can and cannot do. It's great to save money by buying online, but it's better to be able to hear what you buying before you buy it. Aswell, if you get a shop to install your system, buy from them. Very few shops like installing stuff that wasn't purchased from them.
The other thing to consider is the amount of power you want, especially if you want to keep the stock alternator. If you go with too much power, you will kill the alternator. You can add and extra battery, you can add a capacitor, but if your alternator can't provide enough power on its own, it will eventually die.
These are my recommendations on how to choose what to get:
Headunit: Decide what features you want, then choose one that has those features. You may have to compromise to stay within your budget.
Subs/speakers: Listen to a whole bunch of subs and speakers. Decide which sound best to you or meet the needs of what you are trying to accomplish.
Amps: You can run one amp, or multiple. Most 5 channel amps only have a sub channel of 500Wrms. If you want more than that, you will need to go to 2+ amps. Narrow down your amps based on the power of your speakers/subs and the load the amps can go down to to provide power. You will ruin an amp if it is only stable down to 2ohms and you wire it down to 1ohm.
Processors: These are optional, if you decide to stick with the stock headunit, it would be a good idea to get one that atleast will remove the bass reduction that the stock headunit does at higher volumes. The more expensive you go the more things they can do. The MTX RE-Q is popular and not too expensive. Higher end includes the JBL MS8 and Audison BitOne. I wouldn't bother with the BitOne though as it has to be manually tuned and can take even experienced sound engineers weeks to properly tune a car.
Wiring: The wiring you choose will be based off of the power of the system. It's fine to go bigger than required, but don't go lower. However there is no need to go with 0awg if your system only requires 8awg, you're just wasting money that way. Most kits have their power rating on the packaging, if you go that route. If you get multiple amps make sure the kit can support the power of both and you will need a distribution block to split the power in the rear.
Finally, you will require a dash kit, antenna adapter, steering wheel control module (if applicable) anda wiring harness. Metra makes all 3, so that is a good place to start looking. If you get a shop to install everything for you, they will already have all of this stuff.