Yes, set it back on the tires or support it via jackstands in the same locations as the suspension does. Either on the rear end if it's still in or the rear frame rails back in that area and up front close to the control arms/suspension.
Just to give an example, I worked pretty extensively with Car-O-Liner frame and measuring equipment. On their frame spec data sheets there are two sets of measurements. They measure actual production vehicles 2 different ways to obtain the measurements. With the car in frame clamps on the rockers similar to a lift, or with the engine/transmission in or out. So we could put a car on the lift and measure it. Ok, so at the end of the frame rail there might be 5-6mm(1/4?). Picture an imaginary right triangle. One line follows the door gap(let's just say it's a straight verticle line that goes straight up and stops at the top where the door/qtr gap is.) The 90 angle, which is constant and never changes, follows the length of the car out to the end of the frame rail(Let's say it's parallel with the top of the rocker) As the frame rail drops when you lift it, it draws the top rearward opening the door/qtr gap. Cut the quarter off with it hanging and it drops even more. Every piece including the quarters is structural on a unibody. Even with high-tech measuring equipment that's in excess of $30k it's still better to sit them on their suspension to weld the quarter on because the door gap will close up every single time. Old car or new car they droop to some degree when picked up in the middle. If we measured on on it's tires the measurements would all be off because the measurements change at both ends when you set them on their tires. It might not be 100% of the problem but you will gain some ground picking up the ends of the car.
