[KevinH]

You can also start with a custom empty epub layout of your own design.

Create one by using the Tools-> "Create a Custom Empty Epub" menu and you can design the layout of actual physical folders you want for creating an epub from scratch.

I use this feature most often to hand merge two epubs into one when file names would otherwise clash. I unzip both epubs and use add existing to pull in the pieces of one and move it to its folders before repeating the process for the other one.