I'm currently using certificates installed by cPanel AutoSSL (certificates are from Comodo) but I read that I can use CPanel SSL with LetsEncrypt and this is even better. Did anyone use both? which one is better?
Like @BlueLeaf rightly said, they are very similar. The only time I can think it'd be helpful to switch between the two in cPanel's AutoSSL interface is if either Comodo or Let's Encrypt were facing long issuance delays, or experiencing other technical issues, and you needed to get a certificate.
Cpanel auto SSL and cPanel with Lets Encrypt both are free SSL services which provide around 90 days free service. You can issue cPanel Auto SSL from WHM side and Lets Encrypt is third part SSL we need install it manually on the server. We can manage cPanel Auto SSL from WHM side only. Lets Encrypt has cPanel extension which is allowed to us manage Lets Encrypt SSL from cPanel side and WHM side also.