If the databases don't already exist for the other instances, you need to run the Database Configuration Wizard. When you start it, it will ask you which instance you want to work with, and you can then create the database and configure adTempus to use it.
If you already have existing databases that you want to use, you can still use the Database Configuration Wizard to point adTempus to the right database, and have it create a login for adTempus to use, if necessary.
Alternatively you can edit the configuration directly in the Registry under "HKEY_LOCAL_MACHINE\Software\Arcana Development\adTempus\Instances\[instance name]\Database". If you're using integrated security and SQL Server is local, all you need are the "database" and "server" values. If SQL Server is on a different computer or you're using SQL Server security, you will need to configure accounts and permissions as described in the Security Setup section of this topic. If you use the Database Configuration Wizard it should handle all this for you.