Just as in english you could say over as "sobre" when talking about objects over/above something or some place.
Refering to objets located on some place, for example, on the table or on the bed, you can pretty much use both indistinctly. However, it would be much more natural for a speaker if we make a distinction:
For example if you were talking about a blanket being on the bed you could say: "La manta está sobre la cama" or "La manta está en la cama" or "La manta está encima de la cama". We all could understand what you mean, but the first one "sobre" should be better used when talking about the blanket covering most of the bed's surface. And the last one should be better used when talking about the opposite situation as if the blanket was ready to be picked up and not covering anything. The second one could be both depending on the context.
Also you can use "en" when you're referring to something inside another thing. For example in the oven or in the closet should be translated as "en el horno" or "en el armario". So, as you can see "en" is pretty versatile.
Hope I helped!