I rather ftp over file manager although file manager has an advantage I like over ftp and that is when you go to delete a folder and its contents in ftp (I use coreftp) it takes a while to process but if you delete it from file manager it's automatic.
I use WS_FTP for uploading and managing files. The only reason I use cPanel's File Manager is if I need to delete a large number of files quickly as cP's File Manager seems to do this a lot quicker than stand-alone FTP apps.
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If your host has it installed, webdisk is fantastic. A link is saved on your computer and when you double click it, a window of your website's directory is opened and you just copy/paste files there as if you're copy/pasting on your own computer. The only difference is speed of course