The Global Inbox is a separate database from your other databases. There is always a single Global Inbox, and with DEVONthink Pro Office you can have as many additional databases as you wish. Commonly, people will scan documents and place them into the Global Inbox, and then transfer them to groups in other databases.
You might wish to look at Help > Tutorials and view the tutorials on “Using the ScanSnap”, “Scanning Documents”, “Grouping Tips & Tricks”, “Structuring a Database”, “Importing Data”, and others. (These topics were available as of today’s date, and might change in the future.)