We may work in different industries, and I am relatively inexperienced with the system, but regardless I will let you know what I have done. Having a disorganized project list is draining and it takes up too much mental energy to prioritize and sort mentally, and as you have stated there are often many sub projects or connected projects that need to be grouped together. I have found that the best way to keep things together is with the use of tags/areas. I have a separate tag for each client number, and I put the client number at the front of each project associated with that client, and sort my project list alphabetically. I could apply this same kind of logic for projects that aren't client specific, just by tying it to a common general objective/general project. Area's so far I have designated two specific types of workflow which deserve their own area, general workflow, and personal.
Currently I have hundreds of tags, and for projects I assign a
Client number tag
Type of workflow
Project category (type of project, example: follow up, consultation, prior year, current year, etc.)
and then for next actions I just slap on an action specific tag so they can be organized for batch processing, or processing in a specific time/place where it makes sense.
for area's of focus, it's good to assign an area to everything as it just gives you the ability to filter out external "noise" when you are trying to focus on a specific kind of activity. Or if you have job specific responsibilities that should be tracked separately, it makes sense to give it it's own area. In the "collection" and "clarification" process, you view the system without these filters anyway, as well as during weekly (or daily) reviews. But if you are at home or in an environment where you can't do any work, it makes sense to view only the tasks that are relevant to your environment. If you can't do anything about your work tasks then no need to view them at that time, unless you are planning for the next day, otherwise you are putting them on your mind unnecessarily and making your personal tasks feel like a more unorganized mess, because they are cluttered in amongst everything. If you are at work and working on a specific type of task, then it makes sense to view only the aspects relating to that task, rather than sifting through hundreds of unrelated tasks. Filters are optional, but they give added functionality for sorting and work focus.
I hope that is helpful. It's difficult to explain what I mean by "types of workflow" because that is going to be different for every industry. But for myself, the main responsibilities of my job are to make sure clients personal tax is done on time, make sure corporate tax is done on time, and provide general customer service and follow up through out the year. So currently I have an area for personal tax workflow, corporate tax workflow, general workflow, and personal. I'm sure that will change and evolve over time with more experience with the system. But in the short time I've been using the system I already feel like a different person. from feeling overwhelmed to almost feeling in complete control. This system is a powerful skillset and it's clear a lot of people could really benefit from it. There should be a college course on GTD.