Install the interior qtr panel into place with the forward and lower flaps untucked. Once in proper place use some contact cement to glue the flaps to the interior metal (both forward and lower flaps, factory cemented loose vinyl in the rear too). Then you roll over the forward flap (includes the curved section on the bottom) over onto the painted surface of the door jamb without glue.
This way the qtr welting holds the unglued forward flap around the pinch welding. You will probably need to trim the unglued forward flap if it shows under the qtr welting.
Since the lower flap is glued to the metal floor, the carpet is laid on top and is closely trimmed to the interior panel (I put a little contact cement between the carpet and previous glued lower flap).
Then install the door sill on top of the carpet and on top of the lower edge of the qtr welting.
Then you are done with the side

Note: if the installed qtr welting hits the door panel (and door and interior panel are fully aligned) the only way to fix is to trim the metal pinch weld back to give the qtr welting more room.
Here is a pic of my car (convertible) which uses a separate piece of vinyl for that area, but you can get the idea.