We've goten "leftover" characters as allies before, namely Skinbark and Gamling, never heroes. Thus, I personally think we'll see ally Éomer, hopefully Leadership (and reinforcing those Rohan discard decks with Théodred), and we'll probably see his hero version in the next cycle.
I think the last box will include the battle at the black gate. So Eomer won't be left over.
Of course, we don't know for sure at this point, but I would assume that the last box will bring both halves of the narrative together.

