PDF Expert for iOS lets you easily create folders and subfolders as well as move files and folders to organize them in the best possible way. As for the Mac version of the app, it doesn't have a folder structure due to the specifics of the macOS system design - even though you access your files through PDF Expert, they are saved locally on your Mac, organized exactly how you see it in the Finder app.
You can also likewise add a new folder inside the existing one.
Just tap and hold a file or folder and drag it to the destination folder. When you drag one file over the other, PDF Expert offers you an option to create a folder containing these files.
Here's an alternative way to move files or folders: