With containers, most will have a persistent volume that is mapped to the host filesystem. This is where your config data is. When you update a container, just the image is updated(pihole binaries) but it leaves the config files there. Things like your block lists and custom dns settings, theme settings, all of that will remain.

I’m a big fan of duplicati. You can install it on Linux, windows, (not sure about mac) and use it to send backups anywhere. Backup to your nas, to s3, smb share, whatever.