You can definitely add folders to separate out your content.
First, you should know there are two views in the project manager pod. One shows "virtual" folders and the other mostly represents your on disc structure. If you see a folder called "Baggage Files", then you are in the "virtual folder" view. These virtual folders are basically filtered views - the stylesheet one will show your folders structure, but the only files that will appear will be your stylesheet files. To switch between views, there will be an icon in the top left of the project manager pod with a pair of sunglasses (i'm using RH11, but I think RH2017 still has the same icons). If you click that icon, the glasses will change to a globe and the project manager will switch to the file system view.
You can create folders in either view. To keep yourself straight, I'd recommend creating your folders in the top folder that's called "HTML Files (Topics) in the virtual folder view, or "Project Files" in the files system view. I only suggest this, because I've occasionally gotten myself confused when I was creating things in the "Stylesheet" virtual folder and then couldn't see what I was expecting.
Once you've created your folders, you can drag and drop your files into the correct folder. Then when you create a new topic or stylesheet or whatever, do so using the right-click menu on the appropriate folder. This will minimise having to drag topic from the root folder, which is where RH creates files by default.
Hope that makes sense.