Sorry, none of the wiring needed for the upgraded stereo and sub is in the base model. It's pointless to install eight year old OEM gear, when there are plenty of modern aftermarket options that are far superior and will make your old Vibe sound flat. And if you have to pay to have it installed, you might as well get a quality product.
Replacing the radio is easy and DIY, you can order a double DIN from Crutchfield and they'll provide the dash kit and wiring harness adapters you need for next to nothin. You'll lose OnStar with the cheapest wiring harness, but most people don't care about that. I recommend everyone do this, as you'll get better sound just by having a better EQ than the factory radio bass/treble control.
Replacing door speakers is standard Toyota fare. Remove the door panels and drill out the rivets holding the speakers in. Then replace with new speaker rings and speakers. Again, Crutchfield can supply the necessary trim rings when you buy speakers from them. You can install tweeters in the door sill panels quite easily.
The OEM subwoofer panel is impossible to find, so you'll need to get an aftermarket sub enclosure and put it in the trunk. The Rockford P300 is a self contained unit that you can quickly disconnect and remove from the vehicle if you need to haul some stuff.
You could have a five channel amp installed under the passenger seat, and drive the speakers and sub from there instead.
If all this sounds daunting, you will want to speak to an experienced aftermarket car audio shop that can work with your budget to provide the desired result. Don't go to a dealership; they don't deal with car audio.
Check out this YouTube channel to get an idea of what a good shop can and will do for you.
https://www.youtube.com/watch?v=U75ye4JcfAY