After selecting a entity/use code on the customer record in Netsuite it will not automatically apply to existing transactions. You need to make sure the custom body field "Ship-to Entity/Use Code" is shown on your form and populate the correct entity/use code in that field.
Make sure that your custom form has the "Ship-to Entity/Use Code" field set to show.
- Customization> Forms> Transaction Forms
- (Click edit on the appropriate transaction form)
- Screen Fields> Main> (Find field "Ship-to Entity/Use Code")
- Click the "Show" box