Here is a link to a thread describing the custom meta-data method described above.
There are other options, and depending on how you like to plot out this information they may prove more convenient. You have a number of threads you wish to track, this means Keywords or Labels are great tools for this. Keywords can be very convenient because if you open the keyword panel with the Project/Show Project Keywords menu command, select a thread keyword and then click the search button, you’ll get a complete list of every beat/section tagged with that keyword, in the order they appear in the narrative. Keywords are a good choice if your assignments are in any way fuzzy or compound, since you can have many keywords assigned to an item. If a beat involves a collision of two or more important threads, it can be marked for each one of them and show up in all respective searches.
Labels approach things differently (although they lack the automatic search function, you can search by label by changing your Project Search settings by clicking on the magnifying glass within the search tool) since each item can only have one label assignment. We can thus use the colour you pick for the thread can be displayed in lists, cards and icons. You’ll find options for that in the View/Use Label Color In/ sub-menu. Being able to visually see threads by colour coding is something I’ve found hugely beneficial to getting a look at the big picture. I reserve the Label setting for this kind of important information for that reason.
Keywords can also function at the big picture level, but you’ll need to use the corkboard for that, and enable View/Corkboard Options/Show Keyword Colors.
Note that searches can be saved as Collections (again from the magnifying glass menu). So if you have a handful of threads you wish to constantly track, saving them as collection tabs will save you having to set up the search every time you want to switch to “thread view”. Search collections update themselves automatically whenever you click on them.
In summary:
- The best way to work in my opinion is to build your outline in narrative order, or how the reader will be going through the text. (This is your “Whole Thing” list.)
- Use meta-data to call out sections that are significant to a thread, character PoV, or setting location, or whatever it is you need to keep track of.
- Use the various search tools to bring these marked items together into concise lists whenever needed.
It sounds like you might be trying to approach this problem from the other direction—sorting narrative by type and then attempting to turn that into an entertaining narrative with other search and listing tools. That could work, to be clear, but it will be less flexible and in my opinion a bit more difficult to manage (as you say, having to curate that huge Whole Thing collection constantly will be an ongoing pain, and it will greatly reduce your compile flexibility as it will only ever be a flat list of beats rather than a structured outline which can be turned into book structure like parts, chapters and so forth).
Another note: you can “convert” to this way of working rather simply I believe. Since you have things sorted into folders by thread, you can select the contents of each thread folder in turn and batch assign meta-data to the items (not available to custom meta-data). For keywords, simply drag the keyboard from the floating panel onto the selected items to batch assign. For labels, right-click on the selection and use the contextual menu to batch set labels.
This older post may also be of some assistance.