Hello Steve:
The rubber sealing flap on the window glass channel faces the outside of the car. Don't forget to also install the tiny rubber window anti-rattle rubbers. These help keep the windows quiet and well centered in the tracks. One goes on the inner window lip of the body and the second one attaches in a similar fashion to the window trim molding. There are small factory provided slots at these install locations and the rubber is a simple press in fit. The Model 'A' suppliers don't carry the rubber pieces, but the V-8 folks do as they were also used on 32-34 sedans.
A400 Guy