You can always feed in the crate. That way the other dog can't get to the food. Feeding in the crate also goes to teaching the dog that a crate is a safe, fun, relaxing spot.
Separate feeding is better for both dogs. No competition, no potential fights, no food aggression between each other, etc. I've found it to be the easiest way to feed multiple dogs.
A 3 month old puppy is a *baby*. I wouldn't expect her to hold it more than 2 hours at a time or so but I would start with 15-30 minutes and increase from there.
I'd also keep her tethered to you in the house so she doesn't have free range and you have control over her every moment.
Is parvo not a problem where you live? My vet doesn't recommend taking any dog out until they are 1 week past their last vaccination which is at 4 months or so. I've lost a puppy from parvo before so I'm super careful.
Puppyhood is like babyhood. You'll have accidents, you'll have successes. Baby steps.
I can't wait to get a puppy!