Oh man bro man, you are opening a can of worms //content.invisioncic.com/y282845/emoticons/blackeye.gif.66a1670f5aaf7f406e783a63e3387dc5.gif people's opinions vary drastically on this but I guess I will give my 2 cents, keep the 2 cent thing in mind because that is all most opinions are worth....$0.02 not even enough for a dam lollipop nowadays.
From your question I can guess you do not have an unlimited budget so I will start with keeping budget in mind. Get a good grip on what your goals are, you said JLW7AE 12's so I'm guessing you want some nice boom boom. Nice boom boom needs nice electricity. Amplifiers turn electricity into wattage (in a simple way of saying it and understanding it). Start right there, 0 gauge OFC power cables, big 3 or 4. There are articles littered throughout many forums to walk you through that. Deep cycle AGM battery under the hood and/or 1 in the trunk (I almost always add 1 in the trunk, don't always swap the 1 under the hood). Upgrade alternator to higher amperage.
In my opinion this is where to start, fail to do this will cost you in the end. 2nd thing... Accept the fact that maybe some dirtbag is gonna try and snatch yo schnit, accept that and try and be prepared by taking steps as you install to make life difficult for them. Allen screws on subs and other things make it difficult to get yo schnit out of the car //content.invisioncic.com/y282845/emoticons/fro.gif.c695f1f814b01c4ad99fe7f8cccadd29.gif
Subs... Wo there are many options and opinions on this. Me personally, I prefer a custom built single 15 from a member here zueslicious. A 50+ pound beast of a sub that I can throw 3-4000 watts of clean power at. Guess about $4-500 for that sub. My second choice has actually changed recently because the market and technology changes, Sundown X8 or DD SW2508. Both of those are 8" subs, don't laugh... Really don't laugh. 2,3 or even 4 (if it fits in yo budget) of those little suckers in the right enclosure will pound like holy hell, don't laugh I ain't kidding.
Budget, I'm keeping budget in mind here and everything above is where I would start. Budgeting I would actually keep all of your main speakers in place for now, I would add a Rockford 3sixty or Audison bit 1 or bit 10 (buy used) to interface between factory radio and amps. Give the factory alpines a bit more power from another quality amp and dial in the sound with the 3sixty or bit 1/10. You will be very surprised at the end result. Later in the future when the $$ recovers from the above, you can start shopping again for your mids and highs. I do this kind of setup quite often when the factory system is at least from a decent brand. That's my $0.02
Good luck and start a build thread