No, I think you misunderstand how Smart Objects work.
- Duplicate the background layer
- Convert the new layer to a Smart Object
- Double-click the Smart Object. The Smart Object will open in a new window with a .psb extension
- Do whatever you need to do to the .psb image.
- Select File > Save
- Close the .psb window
The changes you made (including any layers you created) will be preserved in the Smart Object. To make further changes, double-click the Smart Object again.