It's safer to use software than using those 3rd party websites, which I have my suspicion may log your username and password details. It's just not safe - and always question why they would be willing to offer that service without any ads (it's not for the good of the public).
Agreed, the cPanel file manager works great. I use it for files under 2GB, as I think that is the limit it can upload, but it works pretty well. There is a choice of two file managers and I prefer the Legacy File Manager as it is quite dynamic with the things one can do with it. One can move and rename folders and individual files, even edit php coding and create an .htaccess file from scratch with it.
One of my favorite features is the possibility to upload an .zip or .tar.gz file, which you can extract very fast.
With net2ftp.com or web2ftp.com it takes much more time.
If cPanel is available, in my opinion it is not necessary to use an external program.
But, thats only my opinion and of course, I accept all other too.