Piggydb is a knowledge building application. You can think of it as a mix of notetaking, outliner and concept map all together, but with the flexibility to do more than that. Its non-linear system and bottom-up or heuristic approach gives you the possibility of creativity to discover new concepts and ideas based on your input. There is no wrong way of using Piggydb. It helps you to elaborate your own knowledge.
Pro Hierarchical tags
Hierarchy for tags gives more flexibility than folders for classifying and structuring your content. It even allows to have parallel hierarchies for the same content using the same tags, connecting your notes together, but in different order. It is up to your needs and creativity.