A VERY simplified layout of the default directory structure. (I've omitted some extraneous stuff).
The "Documents" (~/Documents) directory is placed for your convenience, as are most of the others, like Movies, Pictures, and so on, to aid you in organizing things. You are free to add to that at the root of your User directory or within any of the appropriate existing ones.
For example, within Documents, you may want to create folders for Personal, Business, Financial, or whatever suits you. The entire point is that it's yours to organize how you wish.
The system will attempt to place many file types into a specific directory structure for your ease in finding them later. These are normally the ones that appear as folders with another icon on the face of it.
Unless and until you are confident in changing where things default to, I'd just leave them be. Also, I'd recommend not deleting any of the default directories.