Not sure about the reservation thing. In the past, you could set it up at the booth just before city walk. But the last time I went, they said to visit guest services at the front of IOA to the right, and they set it up.
If you go at night, when you enter Mythos, ask the first person you meet at the entrance for the window seat. Otherwise, they'll assign you to any table.
And yes, I've sat at the window seat at night. It's quite a view looking at Hulk and Dr Doom running. Then we went out back and saw the fireworks. What an evening.