You have two options:
1- If you are creating your ePUB3 file inside our Authoring Studio, you can directly publish it into KNiTO Store. You will then go to the store to add some extra data and metadata and eventually publish it.
2- Alternatively you can add an ePUB3 file of your book from within the store and when you are creating your book. You can download the ePUB3 file and use it to build the book.
Anyway, there is a wizard for this in the Store.