cPanel's backup system supports exclusion files that can omit selected paths from certain account backups.
For an individual account, a file named cpbackup-exclude.conf can be placed in the user's home directory. Entries are paths relative to that home directory, one per line.
Use exclusions carefully. A smaller backup is not useful if an excluded directory later turns out to contain required application data. Document every exclusion so you know what must be backed up separately.