Like you have noted you will just need to bind these to their corresponding column in the cart on your IPN page. How you make this association should not be critical as it will just be what the user sees in their email and will not have any effect on the values that are stored in the db if you are just doing a regular update.
As far as how to associate these values they should come back the same way you set them up on your confirm page, so you can use that as the key and just bind the values from the PayPal post back to their appropriate cart column.
