To upload a file trough the File Manager, do the following:
Log in to cPanel
Under Files click on File Manager.
Choose root and show hidden files, and then click on go.
Click to open the folder that you want to upload files to.
Click on upload from the top toolbar.
Click on browse (some web browsers needs to choose file instead)
Choose the file on your computer the you want to upload.
When you have choosen your file it will automatically be uploaded. You can choose more files while the uploading is ongoing.