So, at the end of Ratatouille after Remy has accepted his place as both a rat and a french chef, he waves goodbye to both his father and Linguini to sleep on the one of the rooftops to get a view of Paris. But where does he live now? Does he go back to the sewers to live with his clan, stay as a pet for Linguini, or does he merely live within the confines of La Ratatouille?
I assumed he lived inside his own restaurant, La Ratatouille, like you mentioned. Because living with either Remy or Django is not fair to the other.
I’ve wondered the same thing too, only i don’t have the answer.
I always assumed that the rat colony lived on top of the chandelier in La Ratatouille.
I like the idea of him living at La Ratatouille, but I can’t say how authentic that answer is.
Maybe Linguini adopted him as a pet rat!
Perhaps the rooftop of LR with his clan. 
You know, I never really thought about it. I guess I assumed he lived above the restaurant with his family, but you’re right, that was never really made clear. On the other hand, I could also see him living with Linguini again, assuming Colette allows that.
Remy lives at his restaurant, of course!