Ideally what should have happened is you have two vcenters.
The first vCenter is to manage the vCloud server Infrastructure and the second vCenter should be integrated with vCloud Director and used to manage the vCloud environment. So any changes done in a vCloud environment are done via the vCLoud director console that then uses orchestration and vCenter to perform the tasks required - create a network, organisation, vapp ..etc.
You can import VM's as vApps from an existing VMware environment into vCloud Director - may be a way around your issue.