The answer is to not use です for existence. です can most closely be translated to English as the verb "to be", whereas あります・います is more closely translated as "to exist" or "to have" (yes, 持つ is also "to have"; translation is not an exact science, and the difference between あります and 持つ is more nuanced of a discussion than I'd like to have here).
EDIT: I just realized the source of confusion. In English, we commonly use the verb "to be" as a shorthand for existence, e.g. "There is a book on the desk" = "A book exists on the desk". In these cases, when trying to think of the sentence in Japanese, you have to distinguish when you are using "to be" as a qualitative statement (e.g. "He is nice") and when you are using it as a statement of existence (e.g. "There is a book on the desk"); the former will use です, the latter will use あります・います. I haven't thought about it extensively, but off the top of my head, it seems to me that "there is" is a good indicator of when you are using existence; without the "there" and just simply using "is", is a good indicator of qualitative "to be".
As a side note, です must always have a subject AND an object. Meaning, in the AはBです sentence structure, A and B must both always be non-empty (your example sentence in the OP had B empty). A can be empty if it is implied through context, but I don't think I've ever seen a valid example where B is empty.