I've been holding off doing a formal tutorial for many reasons, but the primary reason is that while CocoonJS was great if you're making a 100% free game (no ads, no IAP, no buy it now, etc) which is what Bee Active was, without being able to monetize a game with CocoonJS, I decided it wasn't really worth it.
So, if you have any aspiration of making a game that makes you money on the Ouya, CocoonJS is a dead end. As it stands, Ludei has no plans to add Ouya store support, which is a real shame because its like, why bother then? Anywho..
That said, really there isn't much to say on the how too. it was drop dead simple:
1. export a cocoonjs build (not sure if it matters, but go ahead and add the cocoonjs object even though you never need to call on it (i didn't))
2. upload that zip to cocoonjs. I did this with a standard account. nothing i could see in the pro version was worth applying for. NOTE: pro won't let you disable the "powered by ludei" splash at the beginning.
3. compile for ouya of course and be sure you use the canvans+ 2.0.2 which is the latest as of this post. It worked fantastic for me, but I have heard from another dev that it was not good for them. All i know is that it fixed the controller issue for me (you used to not be able to use "on button pressed" before..)
4. download the compiled ouya build. put that apk on your ouya to test things out. I suggest installing dropbox on your ouya using APK extractor which will make an apk you can email from an android device. this just saves you trouble having to move apk's back and forth over a usb drive.. i have a 32gb one installed on my ouya for games so i don't like having to keep ejecting it.
5. you test on your ouya with the signed version to be sure it plays like it should.
6. upload the unsigned apk that came with your signed one to the Ouya store for review. takes about 1-2 days to be approved and you're in. Ouya store stuff was pretty straight forward and I got accepted on my first try.
Ouya is working on a solution similar to CocoonJS using Chromium which ideally would be great because this would be a wrapper for HTML5 games and insure we have the ties to the app store, but they have a lot going on with Unity3D support and other stuff so this might not happen right away, but I feel its something we'll see this fall.
Till then I'm pretty much done with Ouya development with C2 until this solution is worked out. It was a shame to get so close with CocoonJS only to see the final chasm was too great to cross without their involvement/support.