I'm afraid I cannot explain it well enough. I'm a newbie myself, taking up a running installation and trying to upgrade it. Still, I'll tell you what I inherited.
# We create a secret before doing the oc apply
export ca_root="$HOME/github/openshift-platform/clusters/shared_files/root-ca.pem"
oc create secret generic our-root-ca-cert -n $project --from-file=ldap-ca.crt=$ca_root --from-file=bundle-ca.crt=$ca_root
# In the yaml instance definition, we then call to the secret
bundle_cacert_secret: our-root-ca-cert
If there are other steps, I'm not yet aware of them.