OK, it seems a bit cumbersome, but this is how you do it:
Rule One: You cannot change any SQL command that is currently connected to the repository... I'm guessing they feel that this helps keep it safe
A: So, add the command to your report, in the DB Expert. B: Highlight the command in the right hand window of the DB Expert and right click on it. C: Choose to Disconnect from Repository D: Right click on the command again and Edit Command should now be an available choice. E: Make changes to the SQL, and be sure to check the Add to Repository checkbox in the lower left corner if you wish for this to be added back into the repository.
Rule Two: (My two cents) I would always add the commands to the Repository, even though you don't have to. I have encountered issues with editing the command later (after multiple saves, etc) when the command was never added to the Repository.
When adding edited commands to the repository, and if there is no user-level security on the Repository DB, then you are able to save the command with the same name as the unedited version.