Well, first of all, I want to say this for anyone coming here to learn if they are in a similar problem: Socialize the puppy and cat from Day 1. We made the mistake of keeping Apollo away from the cat and that is why we had to work with him leaving the cat alone via "Leave It"
Zeus on the other hand doesn't bother the cats because we didn't keep them seperate, they sniff each other and that's the end of that.
When you are teaching Leave it, I would not switch to the cat until the puppy/dog responds to the Leave it 100% (or very close to) of the time to the command when using treats, or household objects. After that point, then yes, have the cat crated, and let the puppy sniff, then tell him to leave it. Work on this until you see the desired behavior, and then work on it with the cat in the same room as the pup. This will take some time, and quite a few repititions, so patience is key.