When generating a PDF from your bundle, the index will be created exactly in the order that the documents are listed in the documents pane - because of this, you may want to arrange your documents within the bundle into a specific order.
This can be done by either clicking and dragging the documents into the order you desire or, alternatively, you can select a document in the documents pane and then click the arrows found at the top of the pane to move the document up and down the list.