Besides, I think you can use "en" pretty much in every sentence you have to use one of those. If you say "he dejado las llaves en la mesa" is not as precise as "he dejado las llaves sobre la mesa" but it's still correct, and very common to use the first one. I think that's pretty much why we always end up saying "in" instead of whatever is correct in english. So if I were you, I would go with "en" pretty much everywhere

It's not quite as simple as that. It really depends on the context.

not exactly, but may. As you know prepositions are the harder to translate vis a vis 2 languages. EN is locative, so it s ok: en la casa (at home), en el jardín (in the garden) irrespective of what you have inside or outside (i mean the garden or the house). SOBRE is extensively used nowadays but it doesnt imply contact all of the times. so, "el avión vuela sobre la ciudad" (the plane flies over the city - hopefully without contact it) and ENCIMA DE when you want to indicate contact. "el libro está encima de la mesa" (the coffe is on the table). Using SOBRE in this last example is not considered to be a mistake, but it could be a magician who makes the coffee remain it over the table by witchy means.

Yes, you can use on as "sobre" For example: The fork is on the table-El tenedor esta sobre la mesa. But in the case of inside you must use "dentro". My laptop is inside of desktop. Mi portatil esta dentro del escritorio.