The backup part is easy. From memory, it's Programs->LibreELEC->System->Backup. It will create a file that can be copied to removable media. This should always be the first step.
Since you suggest upgrade->create backup->transfer, I assume that the new motherboard is going into a completely new installation, since transfer wouldn't be necessary once an upgrade is done. I would however suggest the first option, create the backup and install LE12 on the new system, then restore from the backup.
I believe that the watched status is automatically carried over in the latest version of Kodi, without the need for AdvancedSettings or whatever it's called (sorry, doing this from memory.) All other settings and info will be carried over.