ApexSQL Audit can monitor scheduled SQL Server Agent jobs but for that either SQL Audit or Trace auditing technology must be used, since the Extended events technology have limitation in the way SQL Server is gathering events into a session file.
So to change auditing technology for the SQL Server that is currently in use within the ApexSQL Audit, please navigate to the Configuration tab, select the SQL Server and click on the Edit button. Here choose SQL Audit or Trace technology:
Also, once the technology is changed, include all operation filters for those SQL Server jobs, or at least use the exact DML/DDL operations specifically selected for those jobs: