1) If you use "at" you have state a specific location. My mother was waiting for me (at) the Olive Garden If you use the "at" in that sentence, you would need to write specific information because a sentence using (at) has to explain what you are doing/location.
1) You could say, " The 200 year old library was located in the center of the city. It was destroyed by a fire last night. or The library which was 200 years old, was destroyed by a fire last night. When you use "city center"- I think you mean the center of the city so if that is what you mean you would use "central" :The 200 year old library which was located in the central part of the city, was destroyed by a fire last night. "City Center" does not make sense because I am still thinking where was it located.
-When you "in" it is a confusing preposition but it means to location or position with(in) something. For example, your tongue is located (in) side your mouth. Or The book is (in) my room.
2) Here is how I am interpreting it: Bodies means more that one, but in the context of this sentence, it would be singular. " The twins were connected from the shoulder to the bottom half of their body.
-Here is where the second half of your sentence might be confusing because you can use both (at) and (in). For example. The twins were connected from the shoulder to the bottom half of their body, and they had their operation at Miami Childrens' Hospital, which is considered to be one of the best advanced medical centers (in) the world.
When you are using (at) there needs to be a specific location(Miami Childrens' Hospital).
Remember at is specific and in means with in something. I hope this was helpful!