The bounding box should be large enough so that any animations don't extend out of its boundaries. Like if you had a character that did a jump animation which actually adjusted its position on the 'z' axis upwards, you would want the bounding box to be taller than the character so that the player fit even at the highest point in the jump. That all being said, though, it's a better idea to just make the jump 'look' like a jump but leave the character in one position and apply impulse in Torque for the actual jump. This prevents issues that can arise with too big of bounding boxes.
To answer your direct question, though, nah the bounding box should just be hanging out in the model. Here's a tried and true example of how to set up the nodes:
| |_ • CharacterModel
|_ • Bounds
To be honest, though, if it's a player that will be controlled by the client I'd recommend to just leave the bounds box alone in the actual art and just set the dimensions for the bounds box in the player's datablock.