If you are REALLY good at partial panel replacement, AND
the lower rear windshield corner is good... then patch them.
If you are not, and/or the rear windshield needs repair,
then, for the best possible results in the least amount of time, I would opt to replace the entire quarter panel with the NOS piece.
While the Quarter is off of the car,
Replace the outer wheel house and the trunk extension...
(with AMD pieces) if available...
I'm sure those two pieces are rotted out at the mating flanges
since the quarter is rotted out there.
If the car is a 2 door hardtop, I would use some square tube welded braces on the door jam to keep it from moving while the quarter is off of the car. If both sides of the car are similar
Do one side of the car at a time...
Make sure your gaps are straight before you remove the quarter and take quite a few pictures of all gaps. Obvioulsy keep the doors on the car....
Best of luck to you....