No, the extra damage from the Darks is added to the total amount of damage that has accumulated after you've completed all the flips and multiplied each heads by 20. So in your scenario with the 2 special Dark attached, for example, a Beat Up that scored three heads would do a total of 80 damage (20 X 3 + 10 + 10).
Edit: Man, 2 in the morning and 2 other people beat me to this as I was typing it. Anyway I guess I can answer the question posed by the Ace about Sneasel being banned. It is not banned in Unlimited and never has been, although it was banned during the original Modified format (which included Neo: Genesis, where Sneasel hails from) way back in the early 2000s. Slowking was prohibited from that as well.