Ok, I have run speaker wires to my Infinity 6x9's in my front doors.
I didn't realize that the rubber boot just slips off the white plastic base/clip that is in the door jam (on the car side). You should go at a corner of the boot with two small screwdrivers. Just sort of peel up the corner of the thin rubber boot. Once you can slip it off of one corner, it will just come off easily. Try not to tear the rubber when you're stretching it with the screwdriver - no sense having holes.
When you are trying to slip/pry off the rubber with the screwdriver, just don't pry up under the plastic with any force or you might snap one of the 4 clips and then it will be a little loose and wont snap back in snuggly (which is what makes a snug water seal).
You can run the wires without taking out the plastic clip, but in order to get the boot back on you will need to take out the plastic clip. It isn't hard, it's just that you have little room and little visibility. Kruzinhi explained it as good as can be explained.
The hardest part for me was snaking the speaker wire on the driver's side. I can't explain it clearly, but from inside the car I could reach in to a small area under the parking brake pedal, and I snaked a wire through the white plastic clip and aimed it towards that area.
All in all it went pretty smoothly. And since I was going through all this trouble, I even soldered the speaker wires to the speakers - and I used 14gauge wire. I do NOT care what other's "think" it sounds like. I care what I think it sounds like.
I still need to run the pre-amp rca's from the PAC to the trunk. And I'll run the speaker wires at the same time (they're just under the floor mats - I'm old so I'm taking a break and watching the Giro). I think I'll run them all up the center under the carpet - that all seems very very easy though. I've installed the PAC aux-in module already, so I'm familiar with that process. And it is very easy. I recommend the small size plastic putty knife to pry off the center radio console, if anyone reading this cars. They have them anywhere (Home Depot) and they work perfectly.
I'm going to remove the aux-in PAC cable though. I don't use it, plus the volume was too low when using aux-in. I've tried different mp3 players, and I have the sensitivity controls all the way up on the PAC module. I've not read any complaints of that, so perhaps mine is bad (I was having other issues with it anyway). I may decide to add the PAC aux-in/iPod cable instead at some point - I don't use or like iPod's, but the rest of the world seems to.