the diode goes on the small terminals of the solenoid. The end of the diode with the band ( probably silver ) goes to the small solenoid terminal that the red yellow / Red white goes to and the non banded end will go on the small solenoid terminal that the red/black goes to. If the solenoid terminals are marked + and - the red yellow should be on the one marked +. I have a feeling your solenoid may not be marked anyway.
You should have a wiring diagram that came with the new controller and if you look at it the soleonoid clearly shows the diode orientation on the small terminals.
Your main switch ( ignition ) at the dash should have a red/white and red/yellow wire attached. the tow run switch should have red Yellow and plain red wires. I cannot recall at the moment how we did the power on and off but i am sure all wires were reinstated where they should be.
EDIT
You should have this diagram that shows orientation of the diode.
https://alltraxinc.com/wp-content/up...2-WIRE-DIA.pdf
And i just saw this that shows how to curl the big cable between the solenoid and alltrax
https://alltraxinc.com/wp-content/up...er_Install.pdf