N99panel panel allows you to upload/manage files/directories via any SFTP compliant client file FileZilla (highly recommended). FileZilla includes many advance features which make most file managers redundant.
Now within N99panel, we have also implemented ‘Dir/Folder Operations’ under user accounts.
From within it, you can do operations which otherwise may not be possible in a SFTP File Manager. These operations are – archive generation (making a zip file), archive extraction and recursive removal of folder tree.
Now if you are running a WordPress based website, there are several file manager plugins available like File Manager ( URL : https://wordpress.org/plugins/wp-file-manager/ ) , Advanced File Manager ( URL : https://wordpress.org/plugins/file-manager-advanced/ ) etc.
If you are work on a Linux or a Mac client, you can also do a SFTP mount on to your local file system. You would need to Google it in order to make that work.