Adding a second Ouya controller to a Cyanouya modded box

I am totally new to all this but I picked up an Ouya in a thrift store with two controllers, I couldn’t get past the Select Network screen so I decided to follow the S-Config tutorial and add Cyanouya. I only want it to play retro games really.

So with great difficulty (I had never even opened command prompt let alone installed an entirely new software), I managed it.

All is great and it works well, however when I try to pair the 2nd Ouya controller it only ever pairs it in the number one slot, so I have both running as number one, I can’t seem to then play multiplayer games on says Snes 9x.

Any ideas?

I would have followed this tutorial, to 1) get past the network screen, and 2) have access to the new store: