When to use a fixative in a drawing with charcoal and pencil?
Workable Fixative is meant to "freeze" what work has been completed already. By spraying when the charcoal layer is finished, before beginning the pencil layer, you "fix" the charcoal layer to minimize smudging of it during work on the pencil layer. There may still be some minor smudging or transfer of charcoal in heavier areas, but it will be drastically reduced from what it would be if you did not fix the charcoal before continuing to work. You will no longer be able to erase the charcoal, and you will still be able to add to it.

There is no real benefit to choosing to wait until the end, unless you believe you will be erasing part of the charcoal during work on the pencil layer. The benefit to spraying as you go is better stability of the materials you've already laid down, as you continue to work over the top of them. If you have areas of the charcoal layer that are complete, these can even be fixed before you move on, as charcoal can easily be worked over the top of workable fixatives.