How can I bulk update the contact employer based on the employee relationship?
You can do this directly in the database by running the following update query:
UPDATE civicrm_contact,
  (civicrm_relationship r 
    LEFT JOIN civicrm_contact c ON c.id = r.contact_id_a) 
  LEFT JOIN civicrm_contact c1 ON c1.id = r.contact_id_b 
  SET c.employer_id = r.contact_id_b,
      c.organization_name = c1.organization_name 
  WHERE r.relationship_type_id = 5 
    AND c.contact_type = 'individual' 
    AND c.employer_id IS NULL 
    AND r.is_active = 1;

This will update the employer field for all individual contacts who have an active employee relationship and do not have an employer already set.