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You can only properly repair rust damage with replacement metal. My opinion and I say my opinion because I am sure there are different ideas about this, but I do not like to replace anymore metal than I have too, while making sure I have gone well beyond the rusted area. If the damage is below the wheel arch I would use a patch panel and cut it in a place that I could also conceal inside the trunk area. If it is above the wheel arch that would mean a quarter replacement to me. I personally do not like partial skins. Too much plastic involved. You would of course need to decide if you have the skills or finances to pay to have a quarter installed. A whole quarter goes to the roofline, under the rear glass, and into the trunk weatherstrip area. That would be the best repair for high rust. Properly installed quarter panels in my opinion do not hurt the value of a car. One way to look at it though. It is rusty and as it is the value is hurt. The quarter panels will never be rustfree virgin panels again. Repairing it is your only choice. The only person you need to make happy with what you do now is you. If you start to sell it some folks may care, some will not. If your potential buyer has a problem with it, then your car just may not be the car for him. It will be the car for somebody. Don't sweat it and just fix your car.