(1) woofers: you don't need a very big hole. 6x9's etc will play fine through a much smaller hole (5" round would be enough), so don't hog out a huge hole if you don't have to.
(2) I would always put something with midrange and treble in the back because that'll get you a real sense of envelopment and spaciousness. There are a number of small surface mount solutions that would require just a small hole or two for mounting. If you don't let your car bake in the summer sun day after day, there are double sided tapes that would be good enough for mounting and would be fully reversible later. The budget solution is to get a 6x9 with integrated tweeter/midrange. The mid/high speakers on those integrated units are usually a little mediocre, but should be good enough unless you're rocking out on Van Halen or Wager operas.
Mounting: top/bottom doesn't matter as long as the seal to the package tray is decent to prevent acoustic "short circuits" where the front and back of the speaker cone are connected via an air path. Personally, I'd try to keep the holes as small as possible (too late for you, right). and bottom mount everything.
Stan, let me see if I have a new set of aftermarket 6x9's lying around. If I find some they're yours. I hope you have some sort of amplifier and an equalizer. The next time we see each other I can show you some data on the acoustics of car interiors. It's pretty bad, and a bit of EQ goes a long long way to making it better. You don't need any of that big showy stuff. Just a little 4x50w amp and a small 8-10 band 4-channel EQ. All of that can be discretely tucked away under the rear seat or under the rear package tray.
