You can send generated files to an automator workflow to organise or post process them after the data merge process. Upload them to an (S)FTP Server, send them by email or do whatever you like.
Additionally, the new automator feature enables you to address other tools to generate data before the merge process. You need some barcodes? Create them with a barcode app (we have an example for that). You want to rotate Images and make them b/w? Do it. There are thousands of Automator actions out there. Create a workflow and use it from within MyDataMerge.