I have done this in just about every vehicle I have owned because I just don't trust other people's work. I have experienced some terrible jerry rigged s**t in my day. I bought a vw bug once that almost burnt to a crisp while I was towing it home because the idiot kid that owned it before me wired the head unit without a fused lead and it came off during the tow. This caused the wire to heat up, melted the coating, melted the carpet, and started a fire. Luckily I had a fire extinguisher in my Silverado and noticed it in time. Lost the rear seat, the battery, half of the carpet, and the passenger side front and rear door/side panels to that kid's mistake. That is one reason you use a fused link on a power wire.
Anyway, it is pretty easy to do. First you find a constant power (or make a new one from the fuse box), then you find a keyed wire, ground it, then start running your speaker wires. The hardest ones can be the the front doors because some vehicles don't give you much room in the boots that go from the cabin to the door. Speaker wires aren't that much of a chore for me because I always have external amps and need to run rca wires and power to them anyway so I do the speaker wires at the same time.