In my 86 k5 I put 6.5 coaxials in the kick panals. It came out sounding really good. If you plan on replacing that factory headunit w/ an aftermarket cd player, you are going to have to trim the dash a bit but its not hard. This I also did. I plan on installing 6x9's in the rear stock locations, modifying the holes a bit to get em to fit right. This location provides good accustics for rear passengers and if you want to sit around on the talegate after wheeling you have good sound for that also. Another option would be to install 6x9s next to the read bench seat. In response to your 1st question, I dont think 6x9s will fit unless they are extreamly slim, because of the window, however I could be wrong. I used the kick panel because its a small area behind the speaker that acts as an encloser providing good bass and midrange response from the speaker.
What kind of gear do you want to run and what is your budget like? Also do you just want speakers or do you want to add in subwoofers to your system?
Sorry this is long winded, hope it helps.
Dustin