You can avoid scratches to the frame by wrapping frame parts with foam pipe insulation. It's cheap, lightweight, and effective if you tape the pipe insulation closed around the frame. You might ask a bike shop to save you the plastic protective pieces that may come with bikes shipped from the factory. One example is a circular piece that attaches to the end of the axles and spread the pressure out over a few inches so the axle or QR end doesn't penetrate the box.