Keep them separated. Yes
And it is really good of you to want to take good care of this puppy.
You can deworm her to give her a jump start, but the worms and fleas will come back in two weeks if you don't change her diet.
there are some people who believe in Packaged dog food.
But nothing is more wholesome that when you make it yourself, if you know how.
I have rescued many German Shepherds in very bad shape by feeding them the following formula: She will love you for it.
Add following items to her diet.
Give her some 1/2 cooked whole grain rice or millet or barley and 2-cups more or less of raw ground beef. To this add one tablespoon of fish oil, either cod liver or salmon.
Add 1/2 tsp of powdered lecithin, some ground flax , some ground sesame seeds,
a grated carrot or beet or broccoli and mix up well.
and last but not least 2 tablespoons of brewers yeast.
It a few weeks, you will have a new dog.
You can substitute raw ground beef for slightly cooked beef hearts, beef kidney, chicken hearts, chicken gizzards,, ground turkey.
You can occassionally give them these items uncooked.
There is a school of thought that dogs need some parasites to digest their food and more.
But Vets will tell you to kill them all.
The jury is still out on this.
If her skin in raw, make a 5% boric acid solution and dab her skin with some cotton cloth dipped into this solution. This will also kill the flease and mites and ticks and is helpful to get rid of mange.
The Vet will use Ivermectin to get rid of her paracites. but I guarantee you they will return as soon as she swallows aonther flea.