Hi @dsm - you can definitely use JSL scripts to add to anything that App Builder does not have drag-and-drop support for. You can create a layout that contains everything that you are able to define statically, and then switch to the Scripts tab. There is a separate script for the Application and for each Module (usually the same as a window). The window, and the statically defined boxes, are created at the point of the statement thisModuleInstance << Create Objects in the script. After that point, you can create and append other boxes, or send messages to the boxes that were created automatically.
Hope that helps!
-Dan