With version 1.0.4 and earlier of the Deployment Toolkit does not have the option of setting the service account used for the various Laserfiche applications. Because of this, it means that in order to follow best practices and use Windows Authentication so you can also use the service account to access SQL, after running the Deployment Toolkit you have to go change the various service accounts and SQL authentication settings.
From what I've read, you can set a service account using PowerShell. It would be great if we could do this using the Deployment Toolkit so we would not have to backtrack as I mentioned above, but it would also enable us to be able to use Windows Authentication for the SQL connections, as we currently can't do that either.