The Story is split up into sagas.  In each Saga their is about 3 or 4 seasons which each contain 4 books.  For example the first book would be Saga: 1 Season: 1 Book: 1.  The Second Book would be Saga: 1 Season: 1 Book: 2.  You'll see when you read.

(Sagas that end in .5 are flash back sagas that take place before the story starts)

Saga 1: The 6th House

Saga 1.5: Neverene

Saga 2: A Vicious Vash

Saga 2.5: 

Saga 3: Where The Soul Goes

Saga 3.5: In the Beginning

Saga 4: Horocrux

Saga 4.5: The Gateway

Saga 5: Men Wolves and the Book of the Moon

Saga 5.5: Samurai X 

Saga 6:

Saga 6.5: The Last Days of Xerxes