I have been playing this game for a couple of weeks and so far I've had a blast, however there are two issues I'm not sure about:
1) what are the dots for on th Task Force display?
2) what are the "damaged" counters for?
The dots on the task force display are to show the basic probability of each zone being attacked using the probability curve of what a roll of two standard six sided dice would produce - that is, a 7 is the most likely, followed equally by a 6 or an 8, followed by a 5 or a 9, etc.
Hopefully whenever you roll a "D12" in the game you are rolling two six siders and not the 12 sided die. That's a fairly common mistake for people new to the game. The designer says in the beginning of the rules what the terminology is that he uses for dice rolls. Unfortunately he's not into pen&paper RPGs so doesn't know about the convention of "2d6".