Ok, just so I know for sure, here are a few questions I need resolved:
My opponent has a Phyrexian negator, he declares the attack. I declare a block with my 4/4 Jotun Grunt. He says "before damage, smother your grunt" I say ok, grunt goes bye bye, do I take 5 from the negator? Or only 1 trample since I did declare the block prior to the smother.
When you assign trample damage, you assign at least lethal damage to the blocker and then the rest to the player (if you wish). Since the blocker is gone, you don't need to assign any damage to the blocker, so you can assign all damage to the player. If the attacker didn't have trample, it would deal no damage to the player, however.
question 2:
I have a face down fathom seer, I attack for with the 2/2. My opponent block with a 2/2 creature of his own. With damage on the stack, if I flip seer, would his creature die and mine live? since seer would be 1/3?
Assuming the Seer has received no other damage, it would be a 1/3 with 2 damage, so it would remain alive.