here's my $.02:
i'd put in a set of 5.25" components up front, and the 6.5's in the rear doors. with 5.25's, you'll be able to move the woofer back a little, and put the tweeter in the same location behind the door panel, so you don't need to do any cutting to the door panel. the tweeter will also be further away from your ears, and closest to the woofer for better imaging

most people use plastic adapters to put 5.25 or 6.5's in their front doors, but i highly recomend using 1/4" wood to make a custom adapter. here's the plastic one:
cheap plastic one
the woofer will be centered, and you might not have enough room to mount a tweeter. even if there is enough room, cutting the hole for the tweeter will make the plastic adapter weak, and you'll loose SQ cause it'll be shaking more. with a wood adapter, all you have to do is trace your stock speakers on it, trace the woofer and tweeter hole, and cut it out with a jigsaw

then you'll have a strong, sturdy adapter to mount components to. when you do this, make it so the woofer is to the rear of centered, so there is plenty of room for the tweeter. you'll also need to seal the wood with wood sealer or paint. if water gets in the door, it'll mess up the adapter if it is not sealed. your other option would be to use the plastic adapter for the woofer, and then cut a hole in your door for the tweeter. for better imaging, you'll want the tweeter in the lower part of the door. there was a pic on protegeclub that showed a nice looking location that was good for imaging, but the site's down

anyways, it was just above where the speaker grill is on the door panel. let me know if you have any questions on any of this

under the seats have a lot of room to fit an amp. you might have to cut off the vents under them, though

also, the momo subs are all marketing. they are definitely NOT worth the money. you are paying for the momo name, not for performance of the sub

for $220 for a single 10, you can do WAY better

it's got a small magnet, it only has a 2" voice coil, and is only recomended for sealed applications

they don't even publish any technical specs on the sub

if you only plan on running a sealed box, i HIGHLY recomend the O-series from elemental designs. it's got a 3 year warranty, like the MOMO, so don't worry about that

i installed an O-series 12 in my friends car, and WOW, i'm not a fan of sealed boxes but it was sweet

granted it only has a 2" VC also, but it's been optimized for sealed application, and it has a larger magnet and i can almost garautee higher excursion too

one of my friend's got a momo 10 in their box when it first came out, and i wan't very impressed. he blew it, and got the newest one, and i'm still wasn't impressed. using their box, we put in a O-series 10, and it was noticably louder

needless to say he sold his momo to pay for the O10

i would also highly suggest an SC10 from resonant engineering.
www.respl.com
for $149 directly through them, it's a great deal. it has the same excursion of the O-series, and it will work great in either a sealed or ported enclosure.