You asked some very good and interesting questions in your D-mail to me, and I am going to take the liberty of moving them here, because I think they would be of interest to people other than just myself, and because here my responses will be subject to "peer review" by others who know more about echinacea growing and breeding than I do. I am hoping that some other echinacea people can respond, to add their insights. But I will respond, as best as I can, to your questions, which follow:
"I read up and now understand how to pollinate the Zinnias and Coneflowers, but what is getting me now is: How can I keep the hybrid going (multiplying) If I get two of the same hybrid plants and cross pollinate them, will they produce viable seed true to their hybrid?
How can I get the desirable traits for the Zinnias (and/or Coneflowers)? (Can you choose them?) Like for example ,how do you choose the color, petal length, ect?
Would it be possible to cross a Coneflower with a Zinnia? ( I am asking because I heard of a new Coneflower that is Blue. The first ever to be blue was created using genes from petunias (I think), and that seemed really cool.)
The offspring of an F1 hybrid are F2 recombinations of the traits (genes) that went into the F1, and for the most part, they are not the same as the F1 hybrid. If you grow a lot of seeds from the hybrid that you like, chances are that a few will resemble that good hybrid, and you can save seeds from them. Actually, if you grow a lot of those F1 seeds, you may actually get a few plants that you like even better than that F1 hybrid that you liked so much. (I have had that experience several times.) By repeating the process of growing seeds and saving seeds only from the plants that resemble your goal, you can eventually "dehybridize" the hybrid and produce a stable strain that comes true from seed.
You can increase your seed yield by propagating your desirable hybrid from cuttings to obtain a number of identical plants (clones) and then get a really big seed crop from your clones. (You could get a much larger number of clones by using the techniques of Tissue Culture.)
"How can I get the desirable traits for the Zinnias (and/or Coneflowers)? (Can you choose them?) Like for example, how do you choose the color, petal length, etc?"
In my zinnia breeding, since I am doing the work, I get to choose what I like. I don't like single zinnias, so I cull and discard them. I don't like striped zinnias, so I don't breed for them. I don't like the classic zinnia flower form, with lots of petals piled closely on top of each other like shingles on a roof, so I breed for flower forms that I do like. But my decisions are, for the most part, purely subjective, and just a matter of personal preference. There are some "objective" components to my goals. For example, closely packed petals provide protection for aphids and some forms of mildew, while open flower forms have fewer "hiding places". I'm not saying you shouldn't listen to others for good ideas about how you might improve Echinaceas, but for your breeding project, you have the final say as to what you like and what you do. If you hope to make money from selling your new Echinaceas, you do need to take into consideration what your customers might like. In my case, this is purely a hobby for my own entertainment, and I totally follow the whims of my personal tastes.
"Would it be possible to cross a Coneflower with a Zinnia? ( I am asking because I heard of a new Coneflower that is Blue. The first ever to be blue was created using genes from petunias (I think), and that seemed really cool.)"
I strongly doubt that you could cross a Coneflower with a Zinnia by conventional pollen transferring techniques. But I have never actually tried it, so I can't be too dogmatic about that. I can say that all of my efforts (when I was much younger than I am now) to cross-pollinate zinnias with marigolds failed to yield viable seed. But the techniques of genetic engineering bring a "brave new world" aspect to plant breeding. I think it is likely that eventually someone will create blue zinnias by transplanting genes from flowers that do have good blues, like morning glories, delphiniums, cornflowers, or whatever. It doesn't surprise me that someone has already done that for Echinaceas, because Echinaceas are a profitable ornamental. My guess is that there is a Plant Patent on the blue Echinacea. It might be economical to propagate such a plant by Tissue Culture. Others are welcome to "chime in" here, because a lot of this is outside my area of expertise, whatever that might be. Oh well, here is a picture of another of my "Echinacea flowered" zinnias.