As far as I am aware you open up the dexnav from the menu where you view your pokemon, pokedex and such and click on the link cable and log on from there.
After that both of you have to press enter at the same time or the other person must press enter within a span of almost 2 minutes after the first one pressed enter.
You need to have the pokemon to be traded in your party(preferably the 1st slot as sometimes you may be unable to move the cursor). Edit: This happens rarely these days.