After several attempts, I ended up dividing the SyncThing folders by device storage and level of trust. Simply put, there are things I don't want on my tablet because it has very little storage space, but I still want small things like my todo list and my keypass database there. Then there is stuff I don't mind having on my work laptop, that's mostly stuff like music or personal things that are not sensitive, like desktop wallpapers (so no private stuff I would minder others at work seeing, and no work stuff I would mind being stolen from my other devices). Then there are things I want on my laptops and desktops, but not on my phone, because they're either too big or only useful on a computer, like downloaded software. That's about it, and this way I only have to think about what to put in those folders, but I don't really add new synced folders a whole lot, and when I get a new device, it's self-evident what folders "should" be on it.
FreeFileSync is for stuff I sync manually, e.g. Firefox and Thunderbird profiles, htdocs folder and MySQL database. The only reason is that if I forget to stop Firefox, Thunderbird, or my webserver before starting it elsewhere -- which I should never do, but it can still happen -- and try to sync, I get a much nicer graphical interface to resolve conflicts en masse.