I did one reciently. Well, a '66, but you get the point. You have to use a large set of channel lock pliers and bend up the roof skin's first 1" or so to get the quarter panel up and under it. Same with the body panel between the back window and the trunk lid.
Once it is place (very hard to do with the quarter window area to work with) you then can hammer down the lips you bent up.
Pay close attention to the trunk gap before you remove the quarter panel too. Have the trunk lid installed and aligned before removing the old quarter. Pay attention to the trunk gap during install. My old quarter gap actually had the lead filler from the factory down into the gap area that I had to replace with plastic filler.
As you melt out the old lead from the factory, pay attention to the area it covers. I inspected the factory lead work before removing, and it was pathetic compaired to todays bodywork standards. You could actually see a large lump under the paint on the top of the quarter. To get my new quarter to blend perfectly to the filler panel where it was once factory leaded, I had to spread filler from the quarter vent area all the way to the quarter end cap and about 8" across the filler panel.
Now keep in mind this fill is VERY thin in this area, but it look a hundred times better than the factory side I have yet to re-do.
Also, use of a rubber mallet is recommended to "nudge" the quarter panel into place. You have to tap it at the rear, forcing it forward. I also had to do some work around the drip rail too.
Late last year I finished a full right side qtr panel on a '69 mach 1 I'm putzing with, which would be virtually the same as a '65.
I'd say it might be a bit of a toss-up compared to a skin. With a full qtr, your not faced with the agony of the infinite (or so it seems) mig welds needed to 'glue' a skin to your join line(s) without warping the panel, and the attending body work to make it ready for paint .
On the other hand, A full qtr involves drilling a significant number of spot welds, not to mention melting the factory lead filled seam (so the spot welds there can be accessed). To add to the misery, the roof panel laps OVER the top of the qtr panel and of course forms part of the trunk and rear window openings.
If you have a spot welder, and were very carefull not to drill all the way through the spot welds with the spot weld cutter, attaching the new qtr is simplified to a degree as you don't need to punch holes in the new sheet metal for plug welding. What will need to be done, is to strip all the e-coat, top and bottom from all the flanges and make damn sure the flanges that the qtr will be welded to on the car are every bit as clean. Otherwise the spot welder will turn out to be a useless heavy lump.
Now all of that is a ton of work to be sure. But the toss-up advantage is that; save for the join line where the qtr mates to the roof panel, little if any finish body work should be necessary on the rest of the panel beyond the usual paint prep stuff.
Hopefully this will give you a bit of insight on which way to attack you car.