First off, my goal here was to do zero modifications to the car and it's wiring system, so no, I did not modify the back deck. The 6x9's drop in, but the screw holes do not match. The factory screws did just make it on the outside of the 6x9's, so I didn't make any new holes, just used the factory screws to hold the new speakers in by the edges of the speaker frame. I added hot glue to be sure there would be no vibrations and the sponge stuff that came with the speakers. I have photos I'll post when I get the chance.
For the connection to the factory wires, I removed the jacks from the factory speakers and attached them to the crossovers on the JBL speakers. This also proved to be an easy place to attach the high-level wires from the Infinity Baselink sub to provide a source for the audio to the sub. Since there are no RCA jacks in the system I'm aware of, I had to use high-level adapters, in this case built into the Baselink. The Baselink also has an auto-sense circuit that turns the sub on without the need for a remote signal wire, so I didn't have to dig into the stereo wires. I did run a power cable from the battery, to the trunk to provide power, it just slipped under a bolt on the battery terminal, no modification needed. I ran it inside the car, under the drivers side kick plates, and into the trunk where the factory wires run. It enters the cabin with the rest of the electrical wires from the engine compartment through the factory boot. That was a real pain and there was a zip tie on the inside that must be removed before you can feed it through. Most people will probably prefer to drill and put a bushing to feed it through, but again I didn't want to modify.
There was all ready a speaker in the left and right side of the dash, but I don't know if I'd call it a tweeter. I also have photos of this speaker and process I'll post soon. It's just a small paper speaker with a cap to filter out low frequencies, it was 4 ohms. It has a 4 hole mounting with one stud and three screws. The center location is empty as only the Bose system uses a center speaker. The jack is integrated to the speaker like the door speakers, so I removed the magnet and speaker parts, then used the basket to mount the new tweeter to. This way it also just dropped in and the factory wires plug right in. The crossover was glued to the bottom of the basket where the magnet once was and i soldered it to the tabs on the jack.
Photos here: http://photobucket.com/Altima2013Speaker