Hi Ryan, I'll try and explain it by using an example. Say one of your echinaceas produced blue flowers but all of the rest were purple. You would sow all of the seeds from the blue one and grow them far away from any other echinaceas, preferably in a greenhouse with anti-insect netting to stop random pollination by bees etc and hand-pollinating them. When the new plants eventually flower, you would keep any offspring which also flowered in blue and discard all of the rest. Collect the seed and sow again, repeating the selection/discard process. After several years (it could take many years) virtually all of the plants will produce blue flowers and at that point you have a stable cultivar. One problem in doing this is that your original blue Echinacea may have happen to have some sort of genetic weakness (say prone to mildew) and you would be breeding this weakness into the new cultivar. There are ways around that by crossing back with a non-blue Echinacea and then going through the selection process again. All in all it can be a lot of work to get to a stage where you could sell the seed commercially (if that is your goal.)
However, there is an alternative as echinaceas are perennial: If you have a special plant, keep dividing it - all of the divisions are effectively clones so you can multiply numbers that way.