What is my bunny doing?

It is t to show its displeasure with something. We have one that thumps when we want to put him back into his cage area after he has run around in an open space. Whether the 2 can be together depends on a few things. First, both must be spayed or neutered, and one must be a male and the other a female. If they are both males who haven't been neutered or both females, the large one will kill the small one or injure it severely. You would need to make sure they get along and not just leave them together. Rabbits are very territorial and most are docile but will fight fiercely for territory. I think it would be safe to keep them apart while you are away from them.