Over here a daily cron job creates a general diary template with some dynamic components like calendar entries imported from pal.
Each project has a separate markdown file in the same relative location per folder.
Project file notes follow the same structure: TOC, People (phone, email, etc), Procedures (for example special invoicing procedures), Projects (structure-first), Current Position (What I'm focused on in recent context), Work Journal (Chronology), and meta-log.
I change the above about once a year in big ways, on average, as I find new tools or ways to organize for better results. The last year's big change was adding the Current Position section which I developed and transferred from position trading.
Note taking from a typical work day follows the Task BATL system, link in profile. It's very structured in terms of indented lists with special symbols for example, and usually list item steps are noted in 2-15m increments and 45-60m work periods.
On average days there is a need to moderate the structure, though, and this is also part of the same task system at that link. I consciously attempt to limit that structure to less time than it takes to complete a normal business day. Otherwise there is no time to be unstructured, which I view as an energy- and perspective-building period.
I use a set of common tags that also help me jump through files in any editor, for example +timesheet IN 3P OUT 330P (30m) Upgrade minor version and review all maintenance services.
At a higher level I have built other tools and shortcuts that help me find and navigate the various text files. The most common example would be a keyboard shortcut that opens a search input with very specific parameters. But I've also built gui tools to easily click and browse sets of files, and panel buttons to quickly open specific files. (In addition to the thousands of journal files and project files, there are hundreds, maybe thousands of files for various topics like Wi-Fi gear in my office, phones, my cats, favorite foods, movies, music, specific hobbies like swl, etc. So there's a lot to search.)
I bounce between my project files and daily journal all day, which also helps me keep my work in context, and avoid getting stuck in an overwork cycle. I have journal shortcuts that place a timestamp and a new heading for me so I can get in periodic resets during the day. A new blank space can be really important for a mental reset.
Hope you end up with a setup that works for you.