How do I care for my puppies incisions? She's a 17 week old German Shepard . I can't keep her still, she loves to run and play.

You will of, course need to see to it that she doesn't chew at the incisions. The problem with trying to cover them is that puppies are more apt to pull off anything that you put on them and eat it. This can cause more problems.
In this case, as aggravating as they can be, an E-collar while you can not closely watch her may be your friend.
Watch for drainage, redness, odor and swelling and give your vet a call if you notice any of this.

You're going to have to be the mean pet owner and keep her cone on and keep her locked up. There is really no way around it. If she is completely amped up and out of control, you can give her a benedryl to help bring her energy down. You can alsp speak to your vet about getting some doggie downers to help you through the healing stages of this surgery.

You're just going to have to deal with it for the next 2-3 weeks