Methodology is all about the tools and processes you use to create an FME project.
One aspect of this is using the tools you have in the way they were intended. If you have experience of software development you might be aware of the concept of design patterns. According to Wikipedia:
Patterns are formalized best practices that the programmer can use to solve common problems when designing an application or system
Design patterns make for a simplified and efficient development process. Likewise, using Workbench the right way makes for a more productive and efficient FME experience.
Additionally, there are other project management processes that you might want to consider using for FME projects, such as prototyping, versioning, re-usability, and peer reviews.