I'm a newbie to making CC but would this be possible? I mean, I'm pretty sure that zombies, mummies and werewolves have their own special skins. So would there be a way to maybe tell S3PE to replace those skins instead of the main ones? At least that's my guess. I am a content noob.

Any ideas? I'd love to be able to change the skins out like we could with TS2.

Zombies don't have their own skin. They are just green sims with special make-up applied on them (wich can be easily selected on CAS) so my guess is you could do default replacement for those. I guess same goes for werewolves, but then again you can make special make up to add more detail, since werewolf form is customizable.
As for mummies, they have their own clothes and hairs, as far as I know they don't use skins, so you could do some default replacement for them too!