You have a couple options for this:
1) Preferred: Setup your batch file in the Guest Customization of your vApp when you are ready to deploy, I provided an example of this in the Custom Deploy vApp package found on the Documents tab of this Forum - in that example, I add a specified domain user to the local administrators group of a windows VM.
2) (Requires SYSTEM ADMIN access to vCloud Director): Lookup the VC:VirtualMachine that matches the selected vCloud:VM object, once located, use the vCenter Guest Operations calls to perform your tasks.
Other options could include things like calling PowerShell to do things for you, SSH, vCenter Configuration Manager, etc...