That's what's great about btrfs. I started using it that way too. It was nice to be able to take instant snapshots of my fs. I just amended my existing backup scripts to act on temporary snapshots instead. Then, I started dividing things up into subvolumes.
I suggest moving your filesystem root to its own subvolume (the convention is to call it @root), then optionally mounting the actual filesystem root as like /mnt/fsroot, and mounting it by passing subvol=/. That is where I keep my snapshots. You can still have /home be nested in @root. I have subvolumes for /var/cache, /var/lib/docker, etc. And more fragmented qemu images just go on a NoCOW subvolume with +C set, and I back up normally.
I also highly suggest reflinks. Once you start using them you will use them all the time.
I don't know if zfs supports reflinks yet, at the time it didn't. But combining reflinks with subvolumes solves a lot of problems. Since btrfs doesn't support recursive snapshotting, you can just do cp --reflink=always -rp @root /path/to/new-subvolume, and it will combine the contents of the subvolumes without consuming any more space. And of course, btrfs-send will (usually) not duplicate reflink data.