My car has power windows and door locks. Take a look at the inside of your doors is there a rubber bit that goes between the body and the door? Look at the attached file it's the black thing in the middle. If your car has that, are there wires inside of it?
If there are wires inside of it then the easiest, and likely cheapest, way is to buy the a used doors that includes the power stuff. Check out
http://car-part.com/" onclick="window.open(this.href);return false; for local wrecking yards. The inside of the door and the interior door panels are the same on the Toyota Matrix, but the exterior sheet metal is different so it won't show up in a cross parts match search (so do a separate search. The 2003-2008 doors are all the same.
For each door you'll need to install the power locking mechanism, power window scissor arm, plug in the wires.
The front door panel will need to be changed with the lock/window switches, unless you are cool with having a hole in the door panel where the window winder was. The rear door panels can take the window switch where window winder arm is now.
If there are not wires in that rubber bit, then you'll also need to run wires to each door for power, ground, window information, and lock information (there might be more wires for each door, I haven't had the Vibe door panel open before. You'll need to follow the wiring diagram for wiring it up. It's available on the internet and we can help you find it if you so desire.