You can choose to generate a separate XML document for each commit. To generate multiple XML output documents, set On Commit to Create New Document. To define the commit, you can turn on source-based commit in the session, or you can generate the commit from a transaction generating transformation in the mapping.
When you create new a document on commit, you need to provide a unique file name for each document. Otherwise, the Integration Service overwrites the document it created from the previous commit.