2. For the Aifon Isle, Broken Sepulcher, and Bradeline's Well, the explored dungeon automatically converts the raw mana (along with any other resource underneath) into an appropriate type which the lair can pick up like a node. Unfortunately, that also means you'll never get any other type of mana from them, but that can't be avoided since you'd have to replace the lair with a mana node, anyway. It should work the same way for the Pyre, too, but I'm not sure since it starts with fire mana.