Each library is treated as a document. You can access them all from Finder based on where you saved them. There is no central list, but EagleFiler remembers recent ones in the Drop Pad, in the Dock menu, and in File ‣ Open Recent. You can also make your own list of aliases if you want to organize them in a different way.
Yes, you can just use the File ‣ New Folder… command.