We currently do all our re-indexing through SQL server (DBCC dbreindex), as it seems to be a lot quicker plus I'm not sure on the JDE side, but it helps to defrag the database. To set it up we just used the maintenance wizard and added a few extra steps to the job to check the database using dbcc checkdb. Also, because of the heavily inserts and deletes we setup to run ever two weeks an update another form of stats is using
sp_spaceused @updateusage = 'TRUE'
This command scans the data pages in the database and makes any necessary corrections to the sysindexes table regarding the storage space used by each table.
You would need to run the update statistic command if you have set in the properties as on, which is the default and should stay on.