I think your talking about the seam between the rocker and the quarter panal, below the rear corner of the door. If so, then dklawsons reccomendation is good. The RTV dosen't have the adhesion to stay in the seam forever, and it'll start peeling out soon. The seam sealer will stay in there for good, and you can paint over it. (it's also available in a squeeze tube at the auto paint store)
If your talking about the seam between the front fender and the rocker, at the bottom of the front edge of the door, then I personally woulden't use any sealer on that. That's a bolt on part, and I would be concerned with trapping water in behind there. There are lots of places on the front fender where water can get in so it needs to be able to get out.