You can use Windows Authentication for logging into your configuration database.
SQL Server supports both Windows Authentication and SQL Server Authentication. Windows Authentication is where you use your windows account to login to the SQL server instead of providing a SQL Server user - this works by linking your Windows account to SQL server. For more information on what Windows Authentication and setting it up please refer to SQL Server help files.
By default a windows account that is an administrator on that computer will also have access to the SQL server through Windows Authentication.
Flow supports the use of Windows Authentication - simply leave the username and password blank when setting up a System Connection and Flow will attempt to login using the details of the user who is executing Flow (ie the user logged into Windows).
Special attention is needed when using Windows Authentication with FlowService. By default FlowService executes under the Local System windows user account. This account has no access to SQL Server therefore you need to modify FlowService to execute under a different account. This can be modified in the Services Control Panel. For more information refer to section Configuring FlowService