Before you start any panel replacement, you should have the body bolted on the frame with shims in place, and all the doors and fenders on to insure the body and door gaps are properly aligned. Be sure to measure the distance from the floor to the cowl at the "a" post, as the "a" post will move both horizontally and vertically no matter what you do.
The next step is to determine what panel to replace first. On my car the original floor and rocker needed replacing. I chose to replace the entire floor first, leaving the rocker on to provide additional support to the body. With the door openings well braced and the doors and fenders off (some people leave the doors on), I lifted the body off onto work horses. The floor was then cut from the body and the edges repaired and prepped as necessary. ( I chose to stitch weld the floor in so I did not drill the spot welds but ground them off enough to separate the seams)
The new floor pan was then placed and loosely bolted to the frame with the original shims in place (except the rubber strips on the frame). The body was mated to the frame with all the other shims properly positioned. I attached all doors and fenders to adjust the body and door gaps to the original configuration. Clamps were used as necessary. Once proper alignment was attained (watch the "a" post which will probably need raising), the body was bolted firmly to the frame and the floor welded and tacked in as appropriate. Areas that were over rubber or not easily reached with the body on, were welded after lifting the body yet once again.
The rocker panels were next, and can be replaced with the body on the frame. My rockers required a lot of metal work to fit properly. A lot of on the car, fenders fitted and gaps checked, more metal banging, some torch work, more checks on the car and on and on. As an aside, I chose to stitch weld the top front rocker flange (forward of the "a" post) to the kick plate rather then separating the kick plate and the inner sill. The floor pans were a piece of cake compared to the work to get the rockers on in a decent fashion.
The important lesson I learned is to go slow, fit and refit, check alignments and check again. It's a lot of work, but very gratifying in the end.
On your project, if the floor pan is a partial replacement it is a lot easier as most of the work can be done on frame. If the entire floor is to be replaced, I would probably replace the fiberglass rocker first then the floor. The new rocker will help support the body when the floor comes out.
I am sure I left something out, and certain others have there own technique, but this process works for me.
Good luck