Natural is a structured programming language, so any design to solve a problem requires the programmer/analyst to be skilled at understanding the requirements and formulating a logical implementation.
Workflow / process flow software may aid in the design phase, and use of tools such as Natural Engineer can help understand the existing workflow / process flow for existing code. Best would be if someone documented the system and its objects in a meta-data repository so that the components can be represented in a BPM tool but that would be quite an undertaking not likely part of your project.
Typically, you need people familiar with all the objects and common routines to best ensure reusability of Natural code.
I would say that Software AG’s recommendations for application and program design are built into their Natural Construct product. Use the object models that are provided and you get a well-structured program/application. I don’t know whether the product documentation would suffice as a design methodology document.