Because you want the cat to be put in the box, you need to say "put the cat in the box", otherwise it could be implying that you want the cat to be put on the box, or next to the box. When you say come here you are demonstrating where you want the person to go with your body. When you say go there you are pointing or psychically demonstrating where you want the person to go. If the place was further out you would have to say go to Sydney, or go to Bangkok because you can not psychically demonstrate where you want the person to go. If you said to a friend over the phone come here you are assuming that the friend knows where here is. If the preposition is known then you can omit it.