Hello Lisbeth,
You will need the Structure Application Development Guide. Part 3 of that document explains all the EDD rules. The guide can be downloaded from the Adobe site. It does not matter which version of FrameMaker - I am using the guide for version 8 and do not even know if there is a newer one.
The structure applications can be found via StructureTools > Edit Application Definitions. That opens the structapp file in FM. Look for the S1000D application and check the name of the template that is mentioned there, as well as the EDD that is defined.
Find the directory that holds these files, create a copy of it and relink the S1000D app to the new EDD and template. Then open the EDD in FM and edit the assignment of paragraph formats to match your unstructured template styles. Import the EDD into the template and save the template. Test it by importing (opening) an S1000D file. Make changes, import de EDD into the template, import the S1000 file again. Keep doing that until you are satisfied with the result.
That is basically it. If you get stuck or completely overwhelmed, send me a couple of files (s1000D format and the unstructured template) and I will make you a reasonable quote.
Kind regards
Jang