[place] + 有 + [thing] [thing] + 在 + [place]
有 and 在 both connect a thing and a place. Which one you use depends on which of the two the listener already knows about.
The first introduces a book the listener didn't know was there. The second is about a book already under discussion, and reports where it is.
What is known comes first, what is new comes last. 有 starts with the place, so the thing is the news. 在 starts with the thing, so the place is the news.
When you're saying where a known thing is, such as 我的书, put it first and use 在. A bare noun with a number, such as 一本书, is new information and goes after 有.
A place followed by 是 and a thing says what occupies that place. 有 leaves room for other things to be there too; 是 says this is what is there.