The files and the Database are the main things so your control panel backup system should be fine.
But since they will be stored on the same server, or the same company server, I will advice you manually move the backups somewhere else. Because even if they have stable servers with redundancy, an account suspension will affect you.
We are actually working on a service to do this automatically.
Experts recommend the 3-2-1 rule for backup: three copies of your data, two local (on different devices) and one off-site. For most people, this means the original data on your computer, a backup on an external hard drive, and another on a cloud backup service.
1. cPanel/WHM Backup: (Home directory and Database separately) You can take a Full backup but will contain everything in that cPanel account, Also select a remote destination in your backup configuration in WHM
2. Using SSH:
/scripts/pkgacct <cpanel-user> --skiphomedir
and then use rsync to sync the home directory to another server. You can write an SSH script and add it to cron to let this happen by itself every day/week or month. (Recommended because its fastest and use fewer resources) My Favorite.
Be advised, if you don't know how to use SSH, do not go for the second option. You might end up with nothing.
For cPanel servers I use the in-built method to backup to an external source.
I also use ClusterLogics (formerly Bacula4) CDP to a different external source.
In addition to the above - there is also on-site backups done daily.
All of these methods have different retention times.