When the configuration " Specify directory during deployment" is selected then you may need to use a deployment tool to deploy this package and need to call .msi for installation.
Hopefully below Microsoft article can help. it has all the command line to install msi.
http://technet.microsoft.com/en-us/library/cc759262%28WS.10%29.aspx#BKMK_SetLogging
Thanks,
Ashish