When you’re ready to go upstairs, you can tell Jackson to “Go crate!” and zip him in.
If he’s slow to go, you can walk toward the crate and continue to say “Go crate!” to encourage him.
Chunk just sleeps on the floor. If he tries to follow you upstairs when you go to bed, you can hold your hand up and tell him “Stay.” Remember not to leave anything out at Chunk-height that he might want to eat, or he will!
If you end up having a lot of trouble with Chunk trying to be upstairs with you (he prefers to be around his people if at all possible) you could either close him in the music room at night, or else close the upstairs doors to the computer room, bedroom, and solarium at night.