To import a database schema you can change to the data perspective. Then in this data perspective you can right click and create new database connection. This will basically import the schema definations from the database that you configure here.
Then right click on this database defination and import it into a project. To keep it tidy you can import it into it's own project and then cross reference this to your message flow project. This should then allow you too auto complete database references etc. and should remove your warnings.
Though it should be mentioned that what you see in the toolkit is only a warning and if you are certain your database references are correct it should work on deploy regardless of these warnings.
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