As far as I know you can’t. YSort works only with its immediate children nodes, so having two TileMaps with YSort (or using a YSort node with the 2 TileMaps) won’t be a solution. For small objects you could use StaticObjects. This way you still can use the YSort functionallity. To make it easier, you should try the Asset Dropper plugin. This plugins allows you to easily add and move you objects to the scene.
The good thing of using the small objects as static objects is that if your player need to interact with them, you can do that. If those objects were tiles it would be rather impossible.