RD, it would be best to run them in the channels GM provided (the same channels exist on both sides of the body, but they need sheet metal covers to protect the wires.
Danchuk has both the front and rear wiring covers for 2 dr cars (#10133 for front at $38.95/pr) and rear (#17607 for $43.95/pr). Pricing is a little odd since the front pieces are longer and more complicated to make than the simple rears... but I suppose that might be based on sales volume or ??
If you run your wires down the middle of the car you'd need a conduit of some type to protect them.