If you're going to cut them on the Jeep, you can measure the arc needed at the topmost suspension compression, measure what you think you need, then tape a piece of string to the hub and use it to trace a perfect arch to cut from. Or if you're going to make a straight cut up both sides, use this method to give you a good rounded arch at the top. If it's too curvy, use more string and attach it under the tire.
then again, if you're using flares, you can use carpet tape or double sided foam tape to temporarily attach the flare to the body and trace the cutout line per the manufacturer's directions.
If you use a sawzall, use a short metal blade. Remove the inner fender liner and double check to make sure you won't be cutting thru anything important, like electrical lines or brake lines.
Some guys will even go to the effort to cut the panel with an extra 1/4" to 1/2" and round the metal off with a body tool or even a hammer to remove the sharp edge left behind by the sawzall.