So, I have all my files that need backing up in ~/data. Within this directory are a bunch of other directories:
I have the home directories of similar name (e.g. ~/Videos) symlinked to the data directories (e.g. ~/data/Videos). This includes some files from ~/.config, symlinked to ~/data/configs/<files>. This means I only need to backup ~/data. I could backup the entire home directory but I don't really want to save EVERYTHING (~/Downloads and all of ~/.config, for instance).
I then have a script that rsyncs ~/data to my FreeNAS, in a backup directory. On the FreeNAS is a jail that runs borgbackup and backs up to rsync.net for cheap backups. (other jails and the freenas itself backs up to a similar directory which also ends up with rsync.net).
I also have a thumbdrive that I plug into my laptop that automatically kicks off a backup script on my laptop for another borgbackup. I don't really prune the thumb drive because it's so large (256GB with the data directory taking up about 100GB).
I'm not sure this is a good way of doing things but I'm satisfied so far. Restoring everything is really easy (copy the data folder from the FreeNAS and then run a quick script to symlink everything).