In the "Files" section of cpanel, you will find an icon called "File Manager", click this and you will be presented with a pop-up asking you to choose the section of your hosting account you wish to view.
The default selection is the "Home directory" which will open the file manager at the very root level of your entire account, showing you all the email folders, statistics folders and other items that really dont need to be touched.
The most common usage is for editing web site files, so for this, you should select the "web root" option, and if you have any .htaccess files, then you should also select the option to "Show hidden files" and then click on "Go".
Now, on the main file manager screen that has opened, there will be a list of all files and folders in the selected directory.
Adding a new folder: At the top of the file manager you will see a folder icon with the following text in bold print; "Create New Folder", click this and on the right side of the page a box will appear where you can type in the name of the new folder you are about to create, and the location that you would like to put the folder in (If you have not selected/highlighted any directories already.
Type in the name and then click on the button labeled as Create. Upon clicking the create button you will see the created folder in "/home/user" (If no other directory was chosen).
Your folder is now accessible and will appear in the list of files and folders.
Uploading files: There is a arrow icon with the following text in bold; Upload File(s). Click on it.
On this newly opened screen you will see 3 upload path boxes all with buttons labeled as Browse across from them. Click the browse button, find the file you wish to upload on your hard drive and double click on it. This will take you back to the screen with the boxes except now you will see the full path to the file you have chosen to upload in the box, and the file will automatically start to upload for you. Repeat this step for any other files you wish to upload.
Once you have finished choosing which files you wish to upload you will notice a line that says; Overwrite existing files: next to a check box. If any of the files you are uploading are already on the server (i.e. uploading newer versions of the file) then check this box. If not then you may leave this box unchecked. As soon as you select your files, they will start to upload automatically.
Modifying the permissions of a folder: First, choose the file/folder that you wish to modify the permissions on. For example, if you wish to modify the permissions of a folder, simply navigate to the directory that has the folder in you want to modify, using the explorer style window on the left, then click on the folders permissions in the permissions coloumn, then click on the "permissions" icon at the top of the screen.
If you wish to completely remove a file or folder and all files stored within it then simply select the folder by clicking on the line of the folder name to highlight it, then click on delete at the top of the screen. The page will refresh and show the file/folder as gone.
Should you want to rename a file or folder click on the actual name of the file or folder and a box will appear where you can type the new name of the folder. After typing the new name, click on the button labeled as OK. The page will refresh and the folders name will now be changed.
Moving a folder: If you wish to move a folder, first navigate using the explorer style window on the left so that the file or folder you wish to move is shown on the right hand window, then "Right click" on the line (not the name) of the file or folder you are going to move and select the move option (Control+click for mac). Then simply enter the path of where to want to move the file or folder to and click "ok".
Copying a folder: Should you want to copy a file or folder to another location "Right click" on the file or folder name and select the "Copy" option (Control+click on MAC), then enter the location you want to copy the file or folder to and click "OK" but note that you cannot copy any file or folder to the same location that it already resides in.