SQLBackupAndFTP retrieves all SQL Server instances of localhost when you open "Connect to SQL Server on this computer" window and you can find them in "Server Name" drop down list. Just click at "Connect to SQL Server" button on main window of SQLBackupAndFTP application to open "Connect to SQL Server on this computer" window and select an instance in "Server Name" drop down list. If you are going to use default instance of SQL Server, just enter "." value into this field.
If you do not see your instance here for some reason, you can enter it manually. Usually, instance name should be like ".\SQLEXPRESS" or ".\SQLEXPR1". You can find all instances of SQL Server in "SQL Server Configuration Manager" tool from Microsoft.