Can a scout work with a Merit Bage Counselor from another Troop, or must the Counselor be part of our Troop?

Yes, it is acceptable to use a Merit Badge Counselor from outside the Troop and even outside the District or Council. In fact when we go to Summer Camp, the Merit Badge Counselors are usually all outside of our Council. Make sure that the Council affiliation is fully filled out on the blue card when he or she signs the card, in case there is ever any question.