I've been getting some questions about how to deal with bonded pairs and litter box issues. Do you separate them? Confine them together? Shouldn't bonded cats be able to share a litter box peacefully?
First, I want to reiterate that confinement should be saved as a last resort. This is the tool at the bottom of your problem solving toolbox, and should only be used once you have tried absolutely everything else, and if the cat in question isn't using the box at all.
Bonded cats are cats that enjoy doing things together. They probably play together, sleep together, groom each other, jointly greet you at the door when you get home. They might fight sometimes, but they don't usually spend a considerable amount of time avoiding each other, and they generally don't take issue sharing their territory or their resources.
These cats should not be separated. If you are at the point where you think you need confinement (check out this pre-confinement checklist to be sure) then I would confine them both to a space that's big enough for them to be happy together.