6.3.1. Solution

Keep the indices of the stacks and freecells outside the main state data-structure and sort the two arrays together. (i.e: in a struct that contains the stacks-and-freecells struct as its first member)
The collection considers only the first sizeof(internal) bytes when comparing two states.
I later used this external information place to store other information like depth in the search tree, the parent state, etc.