Well I cannot tell you my exact procedures, trade secrets and all, but you can definitely get to your goal with either solution. The one problem that I see in your future is the scorching heat down there in AL. I can tell you, with a polycarbonate greenhouse, when the outside temperature reaches 80 degrees it is going to be extremely difficult to keep the temperatures down to an acceptable level for peppers. I struggle with temperatures when its 60 outside if it is sunny. So this limits the amount of time that you can actually keep the plants isolated, too much ventilation is going to introduce opportunites for crosses to happen.
From the research I did before buying my greenhouse I found out that larger greenhouses are actually much easier to control environmentally, much more room for error and whatnot. I think the standard for greenhouses that far south usually involve roll up/down sides which will defeat the purpose. There are a ton of things to consider when building a greenhouse, I highly recommend you do your research and try to take some tours of local, professional greenhouses before you decide what type you are going to invest in.