I followed the Player's Book in the Essentials starter set and mostly finished my character, but it doesn't say what the Misc box is. What is it?
Use the misc column to tally any item, racial, or feat bonuses. Jack of All Trades adds +2 to all skills. Eladrin get +2 to History and Arcana. Just make note of those bonuses elsewhere (feat list, racial box, whatever) so when your GM wants to know why you're +10 in whatever, you can answer quickly and accurately.
the Misc. or Miscellaneous box is intended to hold all the values that aren't explicitly named on the other boxes.
I have not your sheet under my eyes but let's say there's no "enhancement bonus" in the rows of boxes where your defenses are statted. Whenever you wear let's say a +1 neck item, you need to write the enhancement bonus it gives to Fort, Ref and Will somewhere.
That somewhere is, for lack of better options, on the Misc. box
The same goes for racial and item bonus to skills, or extra damage from racial or class features. Whenever you have less boxes than needed to accomodate every different type or source of bonuses, there should be a misc. box.