Best answer: As far as speaker size, in a perfect world any 6x9 speaker will fit your application. However, your biggest factor in a 6x9 speaker will be mounting depth. Usually this isn't an issue but in some smaller compact cars, I've ran into it! So make sure you check! You don't want your speaker to interfere with your window operation!
You will have two options for plug ins, you can use the provided pigtail that comes with the speakers, and attach them to your factory wiring. Or, 9 times out of 10 they sell an adaptor plug so you do not have to cut anything at all! Plug and play!
As for replacing the speakers, you have to buy a pair, might as well install both. You will enjoy the upgraded sound quality!
With 2 way speakers, you have the main woofer, as well as a tweeter.
Where as with a 3 way speaker you have the main woofer, a smaller mid bass driver, and a tweeter.
You can go either way, just depends on what you desire as an end result!
Hope this helps!