You are able to work with separate database connections on separate monitors starting in Workbench 4.5 by following the below process:
1) Open Workbench by connecting to database A
2) Click Connect again to connect to database B
You should now have 2 windows on the left side of the page
- Window 1 - database A
- Window 2 - database B
3) Click the Window connected to database B.
4) Go to View -> Make Standalone Window
You should now be able to move this window (connected to database B) to a separate monitor.