Metanota stores it's local data (notes database, settings and  login data - without the passwords, which are safely stored in the Keychain) in a dedicated folder in your Library folder.

The exact location is the following :

• for Metanota Free : ~/Library/Containers/bogdanf.osx.Metanota
• for Metanota Pro : ~/Library/Containers/bogdanf.osx.Metanota.pro

The "~" sign in the paths above is the standard OSX designator for the user's home folder (like "Macintosh HD/Users/John").

If you want to delete all local Metanota settings, all you have to do is close Metanota, delete one of the above folders (depending on the version you have installed), wait a minute or two and start Metanota again.