Having just gone through this, I have a couple recommendations.
1) Fitting - I see folks suggesting to make your flares match the GT rockers. My GT rockers are such pieces of sh*t I would never make the body of my car match these fiberglass chunks of junk. I know I'll take flames for this, but put your flares where they should be.....centered on the wheel opening. My rockers aren't even the same between left and right. It's very easy to deal with moding the rockers to match your flares. The reason peoples rockers don't match their flares is because the rockers are crap, why use this crap as a critical reference for positioning your flares..........think about it!
2) Cutting - I trimmed the mating surface of the flares to get them to fit the body uniformly. Mine were coursely trimmed and didn't fit very well without some tweaking. Once they fit the body contours correctly, I clamped them in place at the bottom and held them against the body and used a sharpie marker to trace the seam onto the body. You can either remove the flare and cut along the line or leave the flare in place it use it as a guide. I tried both methods and didn't see much difference. If you have an air saw that'll work best for cutting the fender.
3) Welding - I tried TIG and MIG, TIG produced the best results. Mount the flare in place using the butt clamps and when satisfied with the placement, tack weld in between each clamp. I found the most important thing is to take your time and not try to weld too much at once. This will help control warping/shrinking. The time you'll save in hammer and dolly work will be well worth the time spent going slowly with the welding.
4) A couple other tips - I left the bottom of the factory fender in place (along with the factory brace) and butt welded the flare to it. It made for a clean looking and strong bottom edge for mounting the above mentioned rockers. This is hard to put into words, so here's a pic:
Click to view attachment5) I assume your talking about repro GT flares. If so, you'll have to do a little hammer/dolly work to make the bottom of the flare mate to the bottom of the fender. The flare will be flat at the botom and the fender has an angled bottom. I did a gradual morph from flat to angle to mate the bottoms. Again, a pic is worth a thousand words:
Click to view attachmentTake your time and have fun!