I have always done it with inners installed but I never did this on a car I was overly concerned about damaging the paint, or a car with A/C. Taping the edges of the fender and door and laying a towel over the frame where the inner butts up against would add some protection to the painted surfaces. Trying to install the inner with the fender in place is tricky when trying not to scratch the paint on the frame or edges of the fender. Some body shops align the body panels before painting and drill small alignment holes so they can position the fenders back where they were when previously aligned so as not to have to work on aligning them with freshly painted surfaces in close contact to each other risking scratching the paint.
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