I use separate files for separate topics. Org mode is pretty good at linking between files. I've even done coding projects where a TODO list links to lines of code inside of a source file (by grep, not by line number, otherwise they'd go outdated every time I committed).
Getting into Org-mode, I would occasionally run into people who would say, "there's one right way to do this. You should be using Org-agenda view for all of your TODOs, you should be setting up tags with this specific system..." Over time, I have learned to ignore those people.
The main benefit of Org-mode is that it is really, really, stinking flexible. You should use whatever system you're most comfortable with (probably whatever you were using before with Markdown) and then slowly adapt features like auto-archiving TODOs, time-tracking, tags, Org-capture, as you need them.
You should look into them, because sometimes you see something cool like Org-capture and you're like, "woah, I could just hit one keypress, type in a sentence, and it'll get auto-filed for me based on the content." But let that "coolness" factor be the thing that guides you. Org-mode is really big and really adaptable, so if you try to grab everything in one go, you'll end up turning your notes into a chore again.
I started using Org-mode specifically because I hated having to adapt a very personal notetaking style to more rigid commercial apps. And my notetaking style evolves based on what I'm going through in life anyway. Org-mode allows it to be more rigid or more flexible based on life circumstances.