Firstly and foremostly, for ICE installs, you must have the old adages 'Quality over quantity' and 'Bigger is (not always) better'

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How are you going to be putting in the speakers in the front? For a real good quality sound, you will need to get or make some sealed enclosures for the speakers.
6x9's under the rear seats are fine if you're not an audiophile, but strictly speaking, the location of speakers under the rear seats firing into the back of the front seats is far from ideal and a lot of the quality of any sound actually produced by the speakers is lost into the seat.
6.5"s on the rear shelf will be fine, but again you will want to be trying to seal them into separate enclosures to get the best sound. You will probably also need to cut the rear parcel shelf, unless its already been done, of you're going to mount them in pods.
If you want quality from your sound, you NEED to get component speakers. These are speakers where the Mid and tweeter are separate, rather than coaxials where they are all made into the same unit, but these are more expensive than coaxials (well worth the money though).
Amplifier wise, with that many speakers (if you go ahead with 6), you're going to be needing either a very powerful 6 channel amp, or two 3's to drive the speakers to their full potential, and minimise distortion. Distortion can be caused by both an amp underpowering the speakers as well as overpowering them, so getting it just right is imperative.
In my opinion, you're going to want:
A headunit with two RCA outputs to connect it to two amps - the better brands give better sound, so try and go for Alpine, Pioneer etc etc
A pair of good 5.25" component speakers up front in decent enclosures - there are threads in the build section showing you how to make them
A pair of 8" subwoofers to go in a board under the back seats to give you some wobble - these will also need an enclosure to house them.
A pair of coaxials or components to go on the rear shelf. 5.25"s will be fine.
One amp to drive the speakers.
Another amp for the subs.
That will give you very good sound up front (where you want it), some good bass which may be liable to give kidney failure if you crank it up too much, and some half decent sound from the rear.
This will not come cheap however, and to save money coaxials would work fine until you decide to upgrade to components, or not as the case maybe.
For good overall sound you will definitely be wanting a sub.
Its all a matter of opinion though at the end of the day - and also how much you're willing to spend. Some people will say components are the only way to go whereas others say coaxials perform perfectly well, equally some will say you'll get more than enough bass without subs but others can't live without one (or two in my case).