Interesting. I actually have a 98 RAM quad cab also. Its a 4x4 with the sport and off-road packages in case you are wondering. Anyway, I bought the truck about a year ago, and have toyed with the idea of putting a system into it. But the problem for me has been, my ideas get too big. I commend you for putting in a system and yet keeping the rear seat, that's no small task in itself. Im assuming you ardered one of those Q-logic or JL enclosures Ive seen advetised for them?
My idea's start small, some junk under the rear seat, but in no time Im thinking of removing the seat and making walls n crap. *rolls eyes* I have a sickness I tell ya.
Anyway, about mounting 6.5's in a 6x9 opening, it may or may not be possible. You basically can if you can do one of 2 things, cut a little metal to make room for the larger diameter of the 6.5 (vs the 6" center od the 6x9 ellipse). Or, you can buy/make a transition plate. Honestly, Ive never even taken the doors off my truck, but Im guessing there's enough room to add a transition plate. This plate, or ABS plastic braket if you can/do buy an aftermarket mount for that truck, will move the speaker out from the door, therefore allowing it to fit into the smaller opening (due to the basket footprint funneling down the further it moves out.. if that makes sense). This will help with speaker mounting depth concerns, but you must make sure you have room from the front of the speaker to the plastic door panel once in place. Generall, if an aftermarket plastic bracket is made, and most likely is, its possible to do. Id go to your local install shop or best buy, and ask them if such a bracket is available for your truck.
As for the front speakers, although technically what the other poster said is true about round cones being inheritantly strongly/cleaner, there's something to be said for the added cone area of a 6x9 over a 6.5 speaker. Its true an oval cone will deform easier under stress, but in the real world most people wouldn't hear such differences. Im sure everyone here thinks they could and do, but this isnt exactly a good representation of the average joe with a car stereo. And alot of people's ears aren't nearly as discriminating as they like to think (not directed at anyone specifically here). But with that being said, as an owner of one myself, I happen to know 98 RAM's have a nicely placed tweeter on their pillar. There's something to be said for seperating a woofer and tweeter (see above comments about people's discriminating ear), but overall I like the stock placement as it keeps the soundstage high, in your face, where it should be. My only recommendation is, since the tweeters are right there, that you go with a soft dome tweeter to keep those highs from getting a bit too edgy.
For an amp, Id suggest
ebay. You already mentioned
ebay so clearly you know this, Im sure you can find as good a deal there as anyone else here. I was noticing the low prices on some Reference series amps by Soundstream, and their newer Rubicons, on there just the other day myself. Even more premium brands like xtant can be found there for very good prices. If you want new (
ebay is mostly used, although certainly not all), check out
http://www.ikesound.com Ive never used them, but they seem to have a good rep, and their prices are amazing.
Amp brand? Whatever fits your budget, fits your system, has the extras you want and gives you a slight woody every time you look at it, in that order.
Rear fill? Hmm, I tend to agree its not necessary in that truck. But, for anyone in the back, it will sound worse. I suggest leaving the rear speakers stock (or a cheap upgrade if yours are shot) and powering them off the headunit. *shrug* If you wire it right, you should be able to control the volume of the rear speakers independant of the front to balance it out, or even tur off the rears when/if you want.
Good luck and I hope you keep posting here how your project goes, Im interested to know. =]