So there is some confusion on my part to how to calculate the hp for creatures I animate undead on. Do the creatures get d8's or d12's for calculating hp?
Undead use a d8 for their hit dice, and gain bonus hit points from their Charisma modifier.
Also, a creature like a wendigo that the way it moves is by flying, would it retain the flying? I have read it does, I just want to confirm.
That would likely depend entirely on what you animate a creature as. The various undead templates don't necessarily work the same. With just the standard skeleton or zombie template, a creature with magical flight does retain it when animated.