since i'm going to be the only one who will probably be able to give you a legitimate answer besides telling you to put an alpine deck and 2 JL 13w7's in your civic, i'm gonna ask you a couple questions..
what type of car do you have, is it a coupe, sedan, truck, what? this will greatly influence what you're going to do, and get for equipment.
Think about it, what are you going to listen to? is it gonna be a bunch of rap? is it going to be predominantly rock music. What about jazz and easy listening? seriously, these questions are important.
Since you've given no baseline for the type install youre going to do, besides the fact you want to upgrade everything, consider the fact you can save yourself a lot of money by taking some simple steps.
You don't need to upgrade your deck. That's because there is NO need to adjust your bass, treble, and midbass levels, tweeter crossover, LP/HP filters, or any bull shit an aftermarket deck lets you do. Everything can be controlled from the amp, and by skipping this unnecessary step you can throw money into something else that matter. There is an adapter that lets your run a stock radio head unit. I'm not sure what it's called, but its an RCA input adapter, and it pretty much turns your stock radio into an aftermarket deck, for like 10 bucks.
Suggestions for what to get:
-A 5 channel amp. if your gonna upgrade all your components, and add a sub, why not put it all into a contained package. Today's 5 channels are just as expensive as buying a separate sub and speakers amp, and are going to be half the size. While you may not get all that "power" you're looking for, you'll get an awesome performing amp that will be easy and head ache free to install.
-Just get a 15. fuck it. There's no reason not to if you are getting a sub and have the room. 12's suck. 10's suck if you're not in it for sound quality. anything else is silly. if you have the room, find a 15 in a small sealed box, and you will be happy. i promise. i know because i've had multiple 15's all in smalled seal boxes, and i've been happy every time.
-You don't need to get the top of the line speakers. do you know why? because you're running them on a HP filter. the only thing an expensive speaker does is play LP frequencies at high sound levels without distorting. But if you have a shittily burnt cd, or play old music that wasn't made in a basement (early wu tang is notorious for this), your going to send distorted signals to your speakers that might blow them anyway. go cheap, you won't notice a difference, and I really promise that.
That's pretty much it. if this is your first audio venture, don't worry about going as big as possible, you will be so impressed with having just a sub you won't care it sounds like shit. after a while if you still are into it, you might upgrade for sound quality instead of just trying to have the stupidest loud vibrating civic in eastern mass, but that won't come until you grow up a little bit.
but yea, any questions just shoot me a pm, i can guide you in the right direction.