If you are using Clever EDI then, when creating your Container Tracking entries, which is described here Warehouse Shipments then you also will have the option of being able to create them using the EDI Qty Per Sales UOM value.  

The EDI Qty Per Sales UOM Field is available on the Item Reference Entries Page linked to Items.


There will be an additional option available called Suggest Container Tracking and Split Lines by EDI Qty. Per Sales UOM which allows you to automatically create the Container Tracking Entries and split Item lines based on the the EDI Sales UOM value.