It depends how many objects and how many scenes i guess
Another way would be creating entities via script, so you can create them dynamically. But you have to recreate them each time you load the scene storing the name of the object and the X and Y coordinates on the scene's global variable.
Keep in mind that loading the sprite for the objects can take some time (it depends on the size of the image and if it's animated) and the game can froze while loading.
So i think that if there are few objects and few scenes, and you know exactly where you can take/drop some objects and where not, using an entity already created would be ok.
Otherwise if you have a lot of objects/scenes it would probably better to create them via script (using methods and functions). It could be a bit tricky at the beginning but after you have the code you can use it for any object/scene, don't matter how many they are.