I completely understand why the order would be confusing and I apologize for not explaining it in today's lesson! It's one of things I took for granted from making mini books for so long. Let me explain...
Due to the folding along the middle the pages seem to end up flipped from what your mind might assume. And actually it doesn't matter at all which side of the paper you choose to bind so long as you decide before hand (the folded edge or the cut edge). The template is completely symmetrical so it's entirely your preference. I tend to ink all my edges so it doesn't matter visually, but I use the folded edge to bind simply because it's a bit stronger.
Binding along the fold in the middle is what causes the visual "flip flop" of the page. The mini book will layout like this:
As far as the pages go, when you lay them out just decide which side you will bind on therefore which side will be the back after folding. Since I planned my binding margin along the fold, the left side of my page will the back after folding (it might help you to visualize it to actually fold one piece of paper or print out a draft of one page and fold it).
I hope this answers your questions!!!