You snapshot them separately, with snapshots stopping where another subvolume starts. Have a problem booting? Copy the latest /-snapshot. But if for example /var/log is a separate subvolume it persists and you can look up what was wrong.

My setup right now has subvolumes root(mounted to /), home(mounted to /home) , logs(mounted to /var/log), snapshots(mounted to /.snapshots), pacman-cache(mounted to /var/cache/pacman) and swap(for the swapfile obviously).

I do snapshots of root, home and logs (landing in snapshots) regularly that don't require much space (only the difference between on subvolume and its snapshot uses real space in btrfs) and which can all be restored together as well as separately, while losing the temporary data in cache and swap is not problem.

And you can also transfer the snapshots somewhere else as backup (into another brtfs filesystem or as a file), including just transfering the difference from the last one as an incremental backup.