Yes, the joint should be at the bottom. It will allow water to drain out of the sill if any gets behind the rubber.

1950 Chevrolet 3100 (Ol' Roy)

1939 Packard Standard Eight Coupe (The Phantom) | 1956 Cadillac Coupe de Ville (The Bismarck) | 1964 Ford Galaxie 500 coupe |1966 Ford Mustang (Little Red) | 1969 Pontiac GTO (The Dishpit) I 1979 Ford F-100 | 1976 Ford F-150 (Big Red) | 1995 Ford F-150 (Newt)