In my experience, the forum interface does a good job of giving alerts to the threads you are reading, regardless of where they are located.
The problem comes with new threads.
What I expect to see in the general thread is announces to new releases, new ideas, maybe some let's play and general advice. Bugs are usually discussed in the same thread where the discussed release is published, and that makes sense since probably the bug that is pestering you is caused by the last release. It's a good way to curate bug reports, imo, as long as someone remembers to post it later in github.
The problem with the qqqa thread is that, being sticked, it's hard to spot new posts unless you are following the thread and received the alert. Or you have a reason to open it. (I see you have already changed this)
How to install and FAQ, are clearly threads that you don't need to be aware of new comments, but they must be readily available.
The only suggestion I have about the subfolder organisation is to unify them in general purposes.
For example, wanting to learn how to play. Let's say I'm a newby that's is out of the league, where should I look for improving my playstyle?
Currently you have three locations: The sticked tutorial, the Strategy subfolder and the Playthroughs.
I would have all of them in the same place. Call it Learning how to play, how to play, or something alike.
Then, another purpose would be to tweak Vox Populi, which is currently under the two balancing subfolders. This is not just balancing the mod, sometimes new features are being made, or some mechanics are modified to make them better for the user experience. I would put everything related to this under the same folder. Call it Suggestions. Or Balance and Mod Suggestions.
Submods Repository is perfect on its own. It does its job.
Then I would follow the above suggestion to group all the release announcements into the same folder. Call them releases.
So, this is how it would look:
Where to post and forum rules (sticked thread)
1 Release Announcements.
How to install (sticked)
Bug Reports (sticked)
Github Repository (sticked)
Bug discussions and hotfixes in the relevant thread.
2 Learning Vox Populi
Tutorial (sticked)
FAQ (sticked)
Playthroughs folder
Strategies folder
3 Suggestions
Leader Balance
General Balance
4 Mods Repository
Compatible Mods (sticked)
Main threads
Give the option to move posts in the main page to the relevant folder, if they are not generic enough.