Here's what I see happening:
Ok, so Negan recognizes, "This dude is smart and can do impressive stuff, and is a complete coward and so he should be easy to control." And he's generally correct.
So Negan is gonna take him back to his camp, but instead of just beating on him to break him, he's basically already broken. So instead he'll just treat him real well. He'll set him up comfortably, to have him engineer crap. Basically, "Hey dude, you're smart. Work for me, and you can live it up!" Then he'll assume that Eugene will be a loyal dog, since why not?
And then, when he least expects it, Eugene says, "Yeah, this is wrong." and then kills Negan. Probably dies, too, but redeems himself for being a coward through the whole show.