So - and this may not be 100% accurate - Enemy Within is Enemy Unknown + Enemy Unknown DLC + new stuff (missions, character classes) presented as a cohesive whole. The extra content is not "separate" (via code, second disc, or menu option).
I finished both Enemy Unknown and Enemy Within - both are fantastic. If you only get one version, get this one (Enemy Within). Enemy Within does get easier as you continue to play - for a few different reasons (knowing how to manage resources from playing Enemy Unknown didn't hurt). I don't think I've played another game like Enemy Unknown (not that there aren't similar games, just that I haven't played them), so it was refreshing experience.