If you want to update an order field, you should:
1. Retrieve the order model (entity) into a variable
2. Update the model's properties by using "setter" methods
3. Flush the changes into the database if the page controller doesn't do it after finishing executing the action method
These articles may help you to do the above:
-
http://kb.x-cart.com/display/XDD/Understanding+Models
-
http://kb.x-cart.com/display/XDD/Searching+entities+in+repositories
Or do you want to add new fields to the order model? If so you should "decorate" the order model from your custom module and add the necessary fields.