When you're fighting more than one opponent, you decide which opponent you fight, roll against their Speed, do damage to that opponent, and the other one(s) don't hurt you, unless it specifically says all opponents get to strike you. In Book Three, there are lots of fights against many opponents, and while those extra foes don't get a strike against you, you do suffer 1 damage per opponent you're still facing at the end of a round, until you're down to one opponent. But there are also cool new abilities that help you against multiple foes.
In the Headless/Skull combat, the Skull has no Speed and 0 Magic, so it definitely can't hurt you outside of its passive damage (so you may want to kill it first to end that passive damage). And you're right, it doesn't say in the combat notes that items that work against undead work against these foes. But before the fight begins, they are called undead foes, so that may be a mistake. Go ahead and fight them as undead foes.
I love all the questions you have, which reminds me of when I started playing. Keep asking them, if I'm at home with my books, I'll try to answer.