i ran some wires up the front bed post on the drivers side, (it was a different project), there was a round hole in mine & it was near the top of the bed.
I ran the wiring along the door sill, like you mentioned, then i ran it under the carpeting & into the little compartment that is located under the drivers side rear passenger seat, there was a drain hole located there
this is an image of the bed on the passenger side, look at the stake post at the front, you can see the hole in the stake post near the top.
The project that i did was 2 separate power supply sources, they supply power to the Auxiliary 30 gallon Gas Tank Fuel Pump & my Orange Rotating Lights
The switches are mounted in the cubby hole in my dash