The two places that files can be in are the "Files" and the "Projects" Tabs (shown at the bottom of the red box below) of the Files menu (shown at the top of the red box next to the 3dPrinterOS logo).
Files contains any loose files that have been added to the browser, whereas projects contains a folder system to help you stay organized. Most of your files should stay in the projects tab to help prevent a large unmanageable list of files being created as you print more and more parts.
To move files around, first you select them by clicking the check box that appears next to the file if you hover your cursor over it shown in green in the picture below.

Once selected a menu appears at the bottom left of the screen (boxed in blue above) allowing you to print, move, copy, or delete the file. This works in both the projects and files tab of the browser.