Thank you Terry 44 for the quick answers.
So like Freeway Pro would create a “site folder” for you and then within the app you could easily create folders as you need them. I understand what you are saying and so that is not a big deal, as long as I would be able to add/delete/rename the file structure as the project moves along. Would I then just have to have PG “re-look” at the same file structure again and then all is good?