If despatching is happening independently of invoicing you can perform the despatch process either from within the WIP screen or using the factory system. If using the WIP screen the process is as follows:
Select the job then on the Files/Despatch tab click Dispatch . Note that this list would show any existing despatch dockets for this job.
Now enter the Quantity  if different from what was predicted
Select the courier company 
Enter the consignment note details 
Select 'Yes' to remove from WIP 
Click Next  to continue
This will create the despatch docket and allow shipping.