If the document schema property on the Flat File Assembler is blank, the assembler will try to use the schema that matches the message type of the message.
I have built a small project that contains a Flat File receive pipeline (FF Disassembler + Party Validation) and a Flat File send pipeline (Flat File Assembler). This project is deployed into a Biztalk application, I call Common. I can then reference this application from my other Biztalk applications. When I need to send or receive a flat file I use one of these pipelines. I use the per instance pipeline configuration feature of BTS2006 to specify the document schema on the receive pipeline, and almost never specify the document schema on the send pipeline.