On a cPanel server the default server wide SpamAssassin settings are stored in the /etc/mail/spamassassin/ directory.

In my case I wanted to adjust the default spam score of 5 to something a bit higher.

1) Open /etc/mail/spamassassin/local.cf in your favorite editor.
2) Uncomment "required_score 5.0" and update the value to suit
3) Restart the SpamAssassin daemon by running /scripts/restartsrv_spamd

I also wanted to adjust the scores for SPF_PASS and SPF_HELO_PASS as I found the default values to be set too low. The setting for this was found in CPANEL.cf in the same directory, again restarting SpamAssassin daemon is needed after editing this file.

Note: If a user has already specified their own custom score values, these changes won’t overwrite them. User custom scores are stored in the users home directory at /home/user/.spamassassin/user_prefs.