This 9:49 minute video covers the three different output options from the biztalk flat file Disassembler provided in Biztalk. The three options are single detail records without headers or trailers, all detail records together without header and trailers, or all details together with the header and trailer.
This video was made for BizTalk 2004 but should still be relevant for BizTalk 2006 and BizTalk 2006 R2.
Downloading the related sample files might also be helpful. They can be found here: http://www.biztalkgurus.com/files/folders/biztalk_2004_samples/entry15510.aspx
Live Play (no need to download the file) of this video is available here: http://www.biztalkgurus.com/Liveplay/Flatfile/Flatfile_Disassembler_Video.aspx