A common way is to have two (or more) system partitions. You update one, charge the boot one and reboot. Typically the system partition is read only use. The bootloader tries the one it is told to try first, if it finds itself back in the bootloader it boots the other. You have a watch dog that resets if not kicked.

Buildroot and Yoctor give you a few update options. Then there is things like: swupdate.org

And it’s not really that hard to role your own.