You want to be careful of pinching the wire, through the door jam involved too many moving/vibrating/flexing parts that can rub the wire and expose the wire, which can ultimately cause a short, which can cause your car to start on fire. Also, by having that wire through your door jam area leaves it open to the elements. Rain can run down the wire and into your interior or other places you don't want it which can also puddle and lead to premature failure of your wiring, etc. Mold, whatever. Not to mention it looks ghetto as hell. lol.
As soon as I can tear into my car, I'll let you know the best places to run wiring. If anybody is in Texas, I'd be more than happy to help you out too.