it is kind of hard to follow what you're saying completely, but its a bit late here lol
a func_breakable entity in a map doesnt use hitboxes the same way that models do.. in a sense i guess they kind of do, but brush entities in maps basically use the geometry of the brush as the 'hitbox'
if you want to make a wall or a box 'breakable' it has to aleady be a brush entity of some sort (like a func_wall) to change it into a func_breakable, at least as far as i'm aware. This is assuming you are talking about modifying/editing maps that are already compiled into bsp files
not sure if that is what you are talking about