Update: new file manager is now available in the latest cPanel version, the tips below also apply.
Log into cPanel and click on the "File Manager" link. A page will open in a new window.
All of your website files are stored in the public_html directory. To navigate to it (or any other folder) click on the folder image.
Adding a Folder
1. Locate and click the "Create New Folder" link
2. Enter the name for your new folder and click "Create"
Managing a Folder/File
1. Click the folder/file name you wish to manage
2. You will be able to perform some tasks such as deleting or renaming on the folder/file. Clicking on the appropriate link will allow you to perform that task.
Uploading a File
1. Navigate to the directory you would like to upload to.
2. Click browse to find the file you'd like to upload.
3. If the file already exists in the folder you're uploading to and you would like to overwrite it, check the box labeled "Overwrite existing files"
4. Press "Upload"
Change Folder/File Permissions
1. Click the name of the folder/file
2. Select "Change Permissions" from the righthand side
3. You can either check the boxes for the appropriate permissions or enter them manually in the text boxes.
4. Click change to save