This has to be done with two SQL statements, and should be done after the supervisor installation has been performed.
To start numbering new jobs at 1001, run the following:
mysql -u root -e "UPDATE qube.jobidmax SET id=1000; INSERT INTO qube.jobid (id,realid,serverid) VALUES(1000,1000,0)"
This can be done on a running supervisor, there's no need to stop it before executing this statement, but it should be done while no users are submitting jobs.