The car should be resting on it's suspension so there is no distortion or stress on the body.. Hang the quarter panel and secure it with vise grips so you can unclamp and reclamp as needed.. with the door in the closed position, align the quarter panel to the lock pillar to obtain clean straight lines flush with the outside surface.. Clamp it to the rocker panel if at all possible too.. I sometimes use Gorilla tape. Secure the quarter panel to the outer wheel house with c-clamps or (my personal favorite) vise grips so that it will mate evenly all around.. Next would be the trunk drop off at the bottom. As you work your way up to the trunk opening, attach the trunk lid and again, secure the quarter panel for the best lines along the trunk and mate it to the drip flange where the weather strip is located. you can align the quarter panel to the roof in the same manner so the sail panel lays flat into the original pinch weld. The rear window pinch weld must be flat and flush all around to prevent leaks after the glass is installed. By this time the opening at the quarter window will be in line with the inner support panel which can also be secured.. The last area to tack is the outer wheelhouse in case you need to pull it down or shift it left or right.. They are not perfect.
From here, just tweek each area for the best fit.. Once you are satisfied, tack weld at several locations all around.. Do not tack weld in successive lines.. for example, put one tack at the bottom of the lock pillar, one at the bottom of the trunk drop off, one at the trunk opening as you work your way around.. Believe it or not, the panel will shift so keep checking for straight lines.. Most importantly, take your time because you may need to cut a tack weld to preposition the sheet metal..
This is the best method I have found using aftermarket sheet metal to obtain the most pleasing fit.. I use a mig welder, but a flux mig welder will work just as well,, they're just a bit more messy..
Hope this helps..