Think of scope as where the right is on, so the "Documents Only" scope is on the documents inside a folder, not on the folder itself. This is important here because document creation is an action based on the folder you are trying to create the document on, not on the documents inside of that folder. The table here describes what all the possible scopes do: https://www.laserfiche.com/support/webhelp/Laserfiche/10/en-US/administration/#../Subsystems/LFAdmin/Content/Inheriting_Entry_Access_Rights.htm. In your case you want one that applies to folders so that would likely be "This folder and subfolders". 

So if you want to control the ability to create, rename, and delete documents, but not the folders (which it sounds like you are trying to do, not sure why you would need two scopes otherwise), you would set up create documents on "This folder and subfolders", and rename and delete on "Documents only". If you are doing something else, you probably don't need multiple scopes (but please clarify what you are trying to do if so, we can probably set it up).