When you use the AIF file adapter to process messages, you might think that the messages would be processed sequentially in the order they are submitted as determined by the file time stamp (even though the processing is asynchronous). But the file adapter actually uses the file name and processes the messages alphabetically.
So if you want to control the order in which messages are processed by the file adapter, you can do so by creating a sequence using the file name. For example, file names such as PO_000001.xml, PO_000002.xml, and so on. You get the idea. You could potentially create any type of sequence you want.