Resolution:
First run the AppManage utility under TRA/5.x/bin and export the configuration template.
e.g.
AppManage -export -ear c:\NewHireApp.ear -out  c:\NewHireConfig.xml

Then modify NewHireConfig.xml as per your requirements.
Attached is the config file for exporting workflows to the workflow server and deploying the BW process archive for sample project NewHire.
Ti deploy the workflow desktop as well you need to set the Web Application Context below

&ltname&gtWeb Application Context</name>
                    &ltvalue&gtyourContext</value>

And make sure to set the deployment mode to 0

&ltname&gtDeployment Mode</name>
                    &ltvalue&gt0</value>

To use the config file run following command:
e.g.
AppManage -deploy -ear c:\NewHireApp.ear -deployconfig c:\NewHireConfig.xml -app NewHireApp -domain laptop55 -user admin -pw admin

How do I build the deployconfig file for deploying the TIBCO BusinessWorks Collaborator application archive (ear) using AppManage command line utility?