You can do this by right clicking on the server or Databases node and selecting Register Database or by double clicking the Databases node.
Context sensitive popup menu in the Enterprise Manager
This will show the Register Database wizard:
Register Database Wizard, welcome page
Click next to see the needed database and authentication information:
Register Database Wizard, database page
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Alias
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A user defined alias to display in the Enterprise Manager.
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Database
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The full path and file on the server of the database file.
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Username
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The username to use when connecting to this database, this defaults to the username you used when registering the server.
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Password
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The password for the given username.
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Role
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The SQL Role that you want to use when connecting to this database.
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SQL Dialect
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The sql dialect (see InterBase documentation) to use when connecting to this database. This defaults to the SQL Dialect entered in the Preferences of Database Workbench.
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Characterset
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The characterset you want to use when connecting to this database. This is an InterBase connection setting and it has nothing to do with displaying anything inside Database Workbench. You can use the A button next to the drop down box to fetch the default characterset from the database, as used when creating the database.
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The next page of the wizard lists the Database Workbench database registration options.