Enter in Duty costs at IN-B in Duty or Freight in the Costs tab.  Alternatively use IN-L-A.  You need to specify where the freight/duty gets coded to in your GL

That's correct, and works well if using standard costing for inventory.  Not sure how it works if using average costing.  If using standard costing, I would put our best estimate of cost in IN-B.  It creates a credit entry on receipt of the goods to the GL account you nominated.  Then when you get the charge from customs or your freight forwarder, you code that cost to the same GL code.  You then just have a variance from month to month for the difference in your estimate and the actual cost.
Thankfully, where I am there aren't many duties imposed on our imports, but we certainly have variation in freight costs coming across the border.  If the variation is significant, I then query or adjust as required.