Having reference to another assembly is quite common scenario and so is using command line utility to deploy assemblies in production environments where we usually do not have Visual Studio installed.
For deploying assembly, we need to use "ImportApp" command with BTSTask. This command deploys the artifacts inside MSI file and if the application being specified isn't present, it creates it. Also, this command automatically adds reference to other applications. We just need to make sure:
The BizTalk application whose reference is being added should be already deployed.
If the BizTalk application being imported already exists, we would need to use “/Overwrite” switch in Importapp command. [Please see http://msdn.microsoft.com/en-us/library/aa561691.aspx for details about the switches that can be used with this command.