Biztalk 2006 provides the btstask utility to carry out most of the deployment operations from command prompt. However, the help available at the command prompt does not talk anything about adding environment specific binding files.
You can get elaborate information about it on MSDN at this location.-
In order to add the environment specific binding files, you need to run btstask.exe with the -P:TargetEnvironment parameter as-
btstask AddResource -ApplicationName:MyBTSAppName -Type:System.BizTalk:BizTalkBinding -Overwrite -Source:"MyProductionBindingFile.xml" -P:TargetEnvironment="PRODUCTION"