Organize you files
Navigating in the "Project Panel" is exactly the same as in the "Properties Panel", except that here you do not navigate in a hierarchy of layers, generators or modifiers, but in your project tree.
Creating folders and organize your work
To organize your items, you can create folders, by clicking on the icon located on the right of the one adding a new 3D scene.
Moving items to folders
You can click and drag items into the folders, then double-click to go inside.
At the top, you can see in the navigation bar, the current folder and its position in the hierarchy.
If you want to move items to a previous folder, you just have to drag them on the bar, like here to bring them back to the project root.