Mike – I’m sorry to say that I can’t really understand well enough what you are describing to suggest a solution. However, the following link has numerous tutorials for how to create and execute a deployment in BatchPatch. You should be able to use these to model your current deployment.
BatchPatch Software Deployment
If you continue to have issues and would like further assistance, perhaps you can try again to explain as clearly as possible but include screenshots and any other supporting information to help illustrate exactly what you are doing and what is happening. You may contact us to establish an email dialog for this purpose, if desired.