To upload a file through cPanel's File Manager, please follow the steps:
Login to cPanel.
Under Files section, click File Manager.
Select Web Root and Show Hidden Files, then click Go.
Open the folder where you'd like to upload files.
Click Upload from the top toolbar.
Select the file on your local system that you wish to upload.
Once the file has been selected, it will be automatically uploaded. You can select more files while uploads are in progress.