To output a flat file from Biztalk you need to use a send pipeline with the FlatFile Assembler (this does the opposite of the FlatFile Disassembler) i.e. converts an Xml message into a flat file message. It uses a schema that is defined by the MessageType.
If the output file is the same format as the input flat file then you already have the schema, just create a send pipeline and place the flat file assembler component in the assembler stage, build and deploy. On you send port specify this send pipeline on your send port. You should not need to specify the document schema in the assembler as the outbound message should have the BTS.MessageType property set, which is the key to the schema deployed in BizTalk.