I am trying to see the 2nd 3ds code another user has, we've swapped codes but for some reason i cannot see the 2nd one of his. How do i do that?

To see another user's second Friend Code, you must have a second Friend Code of your own filled out in your Friend Code Settings as well (under "Nintendo 3DS Code 2").

What you could do is put the same Friend Code in all three of the 3DS Friend Code Fields, so you can always see everyone's friend code, without worries.