If you can configure it in the UI, then it will be stored in the database. This is true of items, things and some experimental functions where you need to choose which way you define your configuration. You can mix the config where some things are configured in text files, and others through the UI, but this is just likely to create confusion, so I’d probably not recommend that.
If you configure it through text files, then it stays in the text file. Sitemaps and the main rule system are only configurable through text files.
JsonDB is just the backend storage for the UI. In general, it’s not meant to be edited manually, although this is perfectly possible with some limitations and care.
I hope that helps - I can understand it can be a bit confusing and ultimately everything should be more consistent as more OH2/ESH interfaces replace the OH1 systems .