SqlPreindexer -username=scott -password=tiger -query="SELECT name, salary FROM employee" | RemoteEDMIndexer -profile=C:\ExportEDMProfile.edm -result=C:\EDMIndexDirectory\
To add additional switches such as the -separator or -encoding you would firstly need to ensure you specify the -username and -password switches before any additional switches to ensure authentication to the SQL database occurs first so the change in the command would look like this:
SqlPreindexer -username=scott -password=tiger -separator="," -encoding="UTF-8" -query="SELECT name, salary FROM employee" | RemoteEDMIndexer -profile=C:\ExportEDMProfile.edm -result=C:\EDMIndexDirectory\
For more details you can type SQLPreindexer at the command line from the directory path <drive>:\Vontu\Protect\bin to see the switch options are available, you will find more information in Chapter 13 - Using Symantec Data Loss Prevention utilities of your Admin_Guide.