Note, these tips are for the single reactor solution.
If you look at the input mixture, you'll notice you get 3 oxygen molecules for each nitrogen molecules. You need to output a 1:1 mix which means you will require an output to the recycler.
A good first step would be to grab one of each input molecule with either waldo.
So the first waldo should keep inputting and disposing of molecules until it finds an N2, then the next waldo, after a sync, should do the same until it finds an O2.
This will sort through the inputs. An identical route for the other waldo except with a Sync command before it and checking for nitrogen would also help.
The two molecules will need to be put on the bonders, be unbonded, have atoms swapped and then be rebonded and output.
Therefore the logical place for the bonding plates is in the output area.
This places the molecules on the output areas. The blue waldo is first in this example as the red waldo has the Sync command at the start. The blue waldo hits two Sync commands, first to start the red waldo and second to freeze itself on the bonders. The red waldo grabs an N2 and drops it on the bonder and then proceeds.
The red waldo needs to unbond the molecules, grab one of its own atoms and use a Sync command. Then each waldo has to drop its atom in the opposite waldo's bonder. That way both bonders will have a nitrogen and an oxygen. Then they need to be double bonded and output.
This is the end result.