I think water will sit on the plastic sill protecters, the lower ones, not the ones inside the car. If u imagine water comming from the roof, down between door and roof, the big main door seal stops it, so it will trace around the edges of that to the area your on about.
To solve it i cut v notches in the rubber seal on the very bottom of the door, inline with drain holes, this clears up the drain holes and lets water off sills