webcat i will give it the readers digest version as best as i can
in an optimal sound system there is an equal part played by all components. from tweeters to subs there is a huge roll that needs to be filled. there are also many ways to set up the ideal sound system. that being said lets jump to the one that people tend to base it off of....price. you do exert a common concern that most people never take the time to explore before they go out and make a purchase.
subs are a two way market. there is the buyer that wants the best low end bass response and quality sound and there is the other end that most would refer to the high school show off or ground pounder systems. these are fueled by the idea that more power is more sound. while this is true in the lab its based on a sound law that most dont know about or havent looked into. basically its like this, to have double the sound you need 10 times the power running it. with these two factors people tend to buy a 2500 watt amp or higher and also spend the rest of the cash on the matching overly shiney and sparkley sub to go along with it. they dont upgrade the rest of the system and the bass is overpowering and actually looses its appeal when it is just a vibration in a car. then you see them on the cl because they want the cash back to either try again or more often use it on the next newest gotta have thing they have seen that week
6x9s as you ask are a hybrid speaker. they usually have a tweeter or 2 in the center and the cone of the driver is oval shaped. this is to produce the best bass in the space allowed. as stated before this is to save space. also save money in mfg. they do an ok job and most never hear the difference because of all the unique properties each car has to its own design. to actually hear a comparison of the differences between 6x9s and componets you would need two identical vehicles or a sound room. luckily almost all stereo shops have said rooms. as long as you are visiting a reputable one, that also knows what they are doing, you will not see 6x9s in the high end section of a stereo shop. this is because as stated before sound is round, not oval shaped.
it is a better practice to set the budget. then pick the sound quality that you want. the front speakers, being those in front of you are primary. they should be the best part of your system. they create the sound that your ears hear front on and the way a body works. if you go with componets its best to keep them close together. its common practice to put tweeters in the a pillar and the driver in the door. while this is ideal on space allowed it actually messes with how your ear focuses on the sound coming at it. for example if you were listening to a small child with a high voice and a parent with a low voice in conversation that are close together your ear can distinguish that easily. if you separate the tweeter and the driver your ear would hear the child (tweeter) with a distance between the parent (driver). in car audio this is not a tremendous deal because in all distance involved you are still with in a very close area. however if you add a video to your system then the eyes along with the ears will let you know this sound is very unnatural.
rear speakers are for filling the vehicle. more or better speakers = more sound. subs bring the bass, plain and simple. if you think they are not important go home and watch any action movie and turn the sub off. you wont make it through the first explosion before it bores you. all in all try to keep power levels close together for optimal sound 25 watt door speakers and a 3000 watt sub doesnt sound good together. i have been down both roads and like to show off but still have the quality. this is in my s-10 but there is no reason it cant be done in a van as well. if there are specific questions i will do my best to help.