Throughout Parking Spot, he is actively (and loudly) letting the two of them know his opinion on them, and how ill-advised he thinks he it is. But the second he sees Jess upset, he’s automatically, “fix it, dumb-ass!”
And now that they’re official, he’s still not happy with it. Because, yeah, it’s weird for him, and they all live together, and he has to hear them, and see them all the time – and Nick is his ‘go to’ person, his best friend, and he misses his attention, and needs him…
But see, Schmidt’s also the one who forced Jess out to, “get a rebound,” and babysat her on a one-night stand, so she wouldn’t be alone, who wanted them all to take her on a date (Fluffer) to help her out, and who (ridiculously) offered to give her sperm, because “that’s how much I love you.”
And so when he sees Nick doing something stupid (again) in regards to her, despite being weary of them together, he jumps in.
Because it’s not just Nick who is his best friend now ––