1) is there an upkeep phase every round with ancient one, or just one at the beginning?
Yes, there is an Upkeep phase at the beginning of every round during the Final Battle
2) can you trade in between rounds fighting the ancient one?
3) Do during game effects of ancient ones continue occuring during the final round. For example, there is Glaaki, who during the game raises the terror level one if an investigator is devoured. However there is an Epic final battle card specific to Glaaki that lets the first player sacrifice himself to lower the terror level 1 or 3... Which is totally pointless if it just results in the terror level going back up two.
No, once the GOO is awake the "in-game" effects don't count....see Tibs' answer below.
EDIT: Brian got to this one just before me...