You can do one thing.You need to create a custom table add one custom field in customer master to identify EA ordering Customers.Based on this flag the program will identify the Customer and convert the qty into CS.
Similar kind of exercise we did in MM side.Where few of vendors wants the purchase orders information in EA where as some vendors in Ordering unit of measure.However the orders are created on Order UoM (not EA) .So we added one flag in Vendor master to identify to read UoM eaches.
While generation of the Idoc system will check this flag and convert the Ordered UOM qty into Base UoM to Vendor.We are also using ORDERS05 for communicating to the Vendor.You also can do this.
