From what I can see u use the side ports for the inlet,outlet and u need to use the shroud to cover the other of the rad. I gather it would just stick out? I've used the supernova 1260, but I never had a box or anything for it. Hope this helps!
Look at what it's doing. See how it doesn't line up. I'm an Engineer myself so this is very aggravating. Hopefully someone here has one. If I can't figure it out it's going to sit next to my case not in the nice box I bought for it.