You will already have created a database for your Community Edition installation which should be working successfully in the standard single-store mode.
Note that when this section of the guide talks about a "database" what it means is a defined set of tables for a defined user and password. Different database suppliers implement this separation differently but so long as you set up your database so that your defined user can create and access his own tables, you can set up your database as you like. In some cases you may wish to load the KonaKart tables in an existing schema for ease of integration to other applications. So long as there are no database object (tables names etc) conflicts, this is fine.
Now you have to consider whether or not you need a new database for the Enterprise Extensions. The KonaKart Engine Mode you require will affect what databases you will have to create.
Single Store Mode
No new databases are required. The original database set up for your existing Community Edition will be used.
Multi-Store Shared DB Mode
No new databases are required. All new stores will use the existing Community Edition database.
Multi-Store Non-Shared DB Mode
A new database ("schema", "user" etc. - see above) is required for every new store. The KonaKart Enterprise Extensions installation only supports the population of a second store (called "store2"). If you need to set up additional stores in this mode you will have to create additional databases for those and configure the konakart properties files manually. This is easy to do by following the examples that the Enterprise Extensions installation creates for "store1" and "store2".
You will need to populate these newly created databases (that is, databases you create after "store2" which is populated by the installer). Populate them using the konakart_demo.sql SQL script which can be found for all supported databases under the database directory under your KonaKart installation directory.