You should at a minimum have a speaker on the driver's and passenger's door, two tweeters on the dash, and ceiling 'speakers' (which you probably want to rip out). There are also speaker cutouts for two rear speakers on the 'D' pillars (I don't use these. I heard they do nothing for the sound.).
There are places that sell aftermarket templates for speaker for the suicide door area as well as subwoofers or you can make your own. Read other posts on people doing upgrades.
These guys (among others) sell after market parts:
Wicked C.A.S.*::*Magic Boxes*::*Toyota . I used their Toyota - FJ Cruiser Rear PODS. Speaker Pods / Panels
I put two Kicker subs in the back over the wheel wells.
CompVT Sub Boxes | KICKER