I apologize, I want to make sure I understand correctly: You have set of rules in Transform and Cleanse, and you want to apply those rules on different queries? Or do you want to use that same query and rules and apply them to different connections?
If you want to edit the SQL itself, then you would not be able to do that in T&C, I am afraid to say. You can edit SQL, however, in the Data Browser, which you can do by clicking the dropdown button on the upper left, editing the query in the editor, and pressing F9. Keep in mind that you will need to recreate those rules in the Data Browser. Both Data Browser and T&C do let you change the active connection, by clicking the connection item on the lower left of the application and selecting a new active connection while the document is active.