System Save action saves everything - current layout and the state of all game objects. If you only need to save player progress like level number and score, I suggest using Local Storage instead. There are many tutorials, here is one:
If you want to use "System Save", you can add an event which will switch to Menu layout after loading.
System On Load -> System go to Menu
But there may be some flickering on the screen, because your level will still load first before switching to Menu.