You may have to drill new mounting holes, but they will fit in the 6x9 hole. I installed them in a 2009 corolla.
Definitely replace both speakers.
I cut and soldered the wires instead of spending the money for specialized cables.
2-way and 3-way refer to the number of speakers. The large ones reproduce lower frequencies best (like bass and kick drum) and the smaller ones, higher frequencies (like cymbals and high notes on a piano)