If you're ripping both quarters off, I would do some sort of bracing. Skins will cost you $700pr, Full quarters $1450pr......big cost saving and if your metal isn't shot down the gutters, around the window to up the roof, might be worth your while to save that other dough for other panels like the rockers and outer wheelhouses. Also, IMHO..if someone doesn't have a ton of experience, to me skins would be the easier route to go. Mainly because you're working off the old panel placement directly by grafting into it. New quarters, you now need to weld in the proper gap/angle at the Jam, at the quarter window opening, to the roof, in the window opening and corners, along the gutters to the dutchman, truck decklid gap, around the tail light buckets, fill panel and x-member extension. Lotta places to screw up....1/16" over here means 1/8" over there and out of whack 1/4" somewhere else. It can get away from you very quickly. As far as a buttweld down the body, well you have options there. You could run the weld on top of the panels instead of the side, you could flange the old panel and superimpose then weld. Or you could even go the panel adhesive route. Grinding down a buttweld isn't fun, but isn't that hard to do. Yes, you will need some light fill, but you will also need some fill with new quarters as well. But...if you're quarters are shot, well...obviously the answers clear.
No trying to deter you in any manner from full quarters, but be aware they do require a bit more thought and agility to put on without ending up with a crooked car. Going the full quarter route be sure to do a ton of measuring, take a ton of pictures for reference, study the member resto threads where quarters where/are being replaced and don't be afraid to mock up the panels on and off twenty times if that's what it takes.
Blasting is a great idea...gonna save you a lot of time. I would have them epoxy prime it right a way to avoid flash rust. Just touching the metal after blast will create rusty fingerprints on the car.