First off, there are tons of things you can do to assert dominance and train your dog without ever having to give them so much as a swat. How?? Read on

The best thing you can do is to crate train him. Buy a crate that will be big enough for him to fit in when he's grown and keep him in there when you're not around. It sounds mean, but dogs, pups especially, enjoy having a place that they can call their own to get away from everything. Do a google search on crate training and you'll find tons of info on it. Just make sure that as soon as you take him out of his crate the first place he goes is outside. As soon as he does his business outside make a big fuss over it. Act like a fool, anything to get him excited about what he just did! If you can catch him weeing inside, give him a stern No! and then rush him outdoors. If he finishes his business outside, make a big deal of it! When it's time to go back to the crate he will probably whine and howl, but it's essential that you just ignore him. With time he'll figure out that being noisy isn't going to get him anywhere. Also, make sure he has access to his crate even when he's not in it. Some dogs will prefer to get away to their crate for a while even when they're family is around.
Another thing is to take him out way more than you think he needs it. My pup went out every hour until he was completely housebroken. It's much easier to train them to go outside than it is to break them of going inside. Go outside often and keep him in the crate when you're not around.
German Shepherds are herding dogs and are usually very high energy. They're bred to run all day long and out-think a flock of sheep. If you don't find something for them to do, they'll find something on their own and you probably won't like it! Play lots of games, go for lots of walks, just do your best to make sure he's tired. If you can keep his mind busy and his body tired you'll have a lot easier time of the puppy stages.
For chewing, just keep a whole bunch of toys around, but don't leave them all out at one time. Keep three or four out at a time and throw in a different one every now and then. If he starts chewing on something he shouldn't, give him a stern No! and then put an appropriate toy in his mouth and praise when he starts to play. Look for a Kong at your local pet store. They're beehive shaped pieces of rubber that you can stuff with treats. Fill it up with dog food and plug the end with some peanut butter. He'll have to get the PB off and then roll the Kong around to get at the rest of the food. This kept my Collie pup entertained for a good half hour.
As soon as he's settled in and comfortable you'll want to look at clicker training. It's too involved to really get into in a post, but it really does work wonders. You'll start reading about it and think "Man, this is some really hokey crap", but trust me, it works wonders on training a dog quickly.
Finally about dominance. It's important that your pup sees you as the pack leader. There's several ways you can do this. The pack leader controls access to anything good. Food, choice place to sit, attention, water, etc. If you find him in your favorite chair, tell him "off" and then move him. If he tries to jump back up, repeat "off" and move him again. It'll take a few tries, but he'll get it. You can also do a long "down, stay." It's basically keeping the dog laying down at your side until you release him. He'll need to know "down" and "stay" before you could do this of course. Extend the length of the "down, stay" until he can do it for 30 minutes. That's the best non-confrontational way to teach a dog his place in the pack. If that doesn't work, you can use the "alpha roll." If you catch him doing something he shouldn't and he doesn't respond to a stern voice, flip him over on his side and hold him there with pressure just behind his jaw. Make sure you keep a hand available to hold his body down as well. He will flail about and give you a fit for a while, but then he'll sigh and just give up. At that point you can let him back up. Be careful with this though, if you don't do it right you could get bit.
Dog training is something that I love. I've been working with my dogs (2 collies and a border collie) on agility and herding for quite a while now. There's a lot to learn, but it's real satisfying to get it right! Agility is something you may want to think about for your pup as well. If you have any more questions just feel free to ask.
Cougar