Fellow Job Shopper:
 
Our company uses the work order as a collection bucket for the majority of the sales order costs.  We may have more than one work order for a sales order when the customer requests various delivery dates to employ the Just in Time concept for material.
 
This practice allows us to use JC-A, Job Cost Report Summary, to show profitability for the work order(s). Extra costs (freight, import duties, etc), WO-H, are included here as part of the job cost.  Our IS employee also created a Crystal Report for management to track rate of return which gets its info from JC-A, the crystal report just performs additional calculations for return rates.
 
Various items like outside set up, tooling and testing costs, paste stencils, etc. flow directly to COGS instead of the work order, but can be added manually to arrive at a total sales order cost.  These items usually pertain to a customer's specific product and will benefit any work order created to manufacture this product over its life cycle.
 
Question - why do you create a new work order just to add in extra costs after the sales order has been invoiced?  Extra costs can be entered at any time, they just won't pass thru to sales order and inventory costing if entered after the last shipment is made, but wil allow you to track profitability if maintained in the same sales order work order.  Extra costs can also be billed to the customer separately as a noninventory part number - for example an expediting fee, paste stencil - we usually bill these extra costs with the first shipment, but can be probably be billed at any time.

Extra costs can be posted to work orders to manufacture type A (subassembly) and F (finished goods) work orders and thereby, these extra costs become part of the WIP calculation when reporting finished production.  In turn, it is these finished productions costs that pass through to the Sales Pre-Post Report (cost of goods sold) when the item ships.  This info is more than just a piece of paper, because it is these figures that appear as Cost of Goods Sold in the Sales Journal.
 
Your extra costs of freight, warehousing, etc. can be added to the manufacturing work order and will appear as part of the WIP cost, and will be transferred as part of the inventory cost when reported to finished goods.
 
My statement to manually add extra costs refers to your data collection process of costs or tool for measuring sales profitability, such as an accounting spreadsheet.  No, I do not perform a journal entry for these items.
 
Also, our purchasing agent uses the work order BOM when procuring material, and does list the work order numbers for each part number ordered. When a part is purchased for more than one work order, notations are made to show the distribution qtys. for each work order number, and the balance to stock. These aids in receiving material as this individual also performs the work order issue of material.

We use a lot of "N" types.....  
 
If  you have your "N" types set up with your ASSET account and COGS the same account, the invoice post is a wash, no matter what $$ value it is.  The cost of purchasing an item or finishing a WO for that item is already in COGS (because your asset account is your COGS account).  
Changing the last cost before posting will make the profit report on a sale correct, which is why we also try to do this step before posting the sale of an "N" type that we make  or a generic ''N' type that has many different costs when purchased.  
 
Hope this helps in regards to "N" types!