Unfortunately, this will not be as easy as you might imagine.
The Flat File Disassembler will not create a hierarchical structure from a flat structure.
You will need to create a Flat file schema that has the same structure as the your data
i.e. multiple records containing every field.
You can then use a map (custom Xslt using Muenchian grouping) to group into a hierarchical document structure.
You can then pass thru a pipeline to debatch the documents ( the output schema for the map will need to be an envelope/document schema) and this means sending the file out a send port and receiving in another receive port.
Alternatively, you can debatch the the output of the map inside an orchestration.
This would all be easier if the output from SQL was already in a hierarchical document structure. Do you have the ability to change the extract mechanism from SQL or do you have to work with the current output.