In addition to the other excellent guidance from @mwra @PaulWalters @MartinBoycott-Brown @Sylvaticus @latinhypercube @doublem @amahabal @satikusala and others here, let me add the strongest possible emphasis to the point above.
Hierarchy is a natural style-of-organization, for those of us accustomed to working in outlines, in classification structures, and in many other forms of work.
In Tinderbox, hierarchy is usually not your friend.
The challenge with hierarchical organization is that any individual note can exist in one and only one container. It can have only one “parent” note. It can have only one “descended from” path. In a map view, the “original” note, ie not an alias produced by an agent, can appear on a map only with others within that same container.
In “normal” outlining, that discipline of a strict hierarchy is often useful. But in Tinderbox, where you often want any individual note to have a wide variety of connections and be part of various linkages, tools other than the hierarchy itself are generally most useful.
For some people, the most useful way to make those connections is through links. I don’t use links that much.
For others, including me, the most useful organizing tool is a range of attributes, whose results as displayed either through the Attribute Browser or via agents (whose results are shown in resulting outlines, map views, time lines, attrib browsers, or whatever).
The trait that links all these different approaches is “virtual hierarchies,” and “virtual containers.” Ie, in “normal” hierarchies you might have a certain note included in an “Events” container–but you might also want to view it as one of several items within a “Calls to Make” container, or an “XYZ Company” container, or a “Major Projects” container, etc. If you use attributes–fundamentally, a more flexible version of “tags” or “keywords”–rather than normal hierarchies as your main organizing tool, you can create any virtual hierarchy you want.
If you check back on this thread from several years ago, How to use the Attribute Browser, you will see a lot of more detailed explanation of using the Attribute Browser.
What does this mean in practice? For me, most of the notes I enter are in the same catchall container, “Entries” or whatever, depending on the file. The only ones for which I create additional containers and hierarchies are where there are very specific sub-steps or sub-elements for an item. Eg, note might be: “Plan for Trip to China,” and the sub-steps would be “Check China visa” and so on.
The TL;DR of this whole post is: Even if your natural inclination is, like mine, to think of outline-style hierarchies as a basic thought-organization tools, recognize that Tinderbox is often at its best when least hierarchical.