1) when you place a creature into your war council (and he's not assigned a spot on the scenario), where can you put him on the board to start? anywhere in the first 4 rows?
Depends on the way you play the game. The creature placement rules for regular scenario play are in the basic rulebook, just look them up. For Call to Arms you have to place the creature on the spot indicated on the card unless neither player has such a card, in which case the above rules are invoked again.
2) why does dragons come with the troll card? just to taunt me, or is there a way to get it into play?
Customer service. The Troll expansion lacked the cards, so they put them into the next explansion released. You can just ignore them.
3) how many creatures can you have on your council? i see there's a space for a guest, but haven't seen it mentioned in the rules anywhere.
You can theoretically have 3 level 1 creatures. All creatures without a level printed on the card are considered level 1. The guest spot is for the heroes explansion.