I ran MatterControl as 'Root' and still have problems. When I re-scale an object, then hit save as, it changes the icon to a question mark. If open the file folder, I see an '.AMF. file, but attempting to view gives me a blank preview screen.
Yes. Load your first model into MatterControl, then go into Edit mode. You can then drag and drop additional STLs into the edit view, and they will be added to the same print. You can also hit copy to print more than one of the same object.