Serious Question...how do you discipline a dog?

Joe and I are having some great sneak peaks at parenting by having dogs. Coby has been a little jealous of Otto and all the attention he is getting...so last week he acted out a little...by destroying the comforter on our bed:

I was at work when this happened, so Joe is the one who discovered this and he was not calm in his reaction. I only know what he told be but apparently he yelled at Coby a lot, the dog got scared and ran away from him (falling down half the stairs when he fled) and then Joe tied him up outside to think about what he had done. I thought, oh our poor baby is feeling jealous and he is acting out to get attention. I will give him some attention and then hopefully he won't act out....I took him to Petco when I got home and we got treats and a new toy.  He hasn't acted out since but we're not sure who's strategy worked...

Also, Otto has not been an angel lately either. He discovered his voice and at times the constant yapping is very trying on my patience no matter how cute he is.  I have accepted the fact that we need to take him to an obedience class. (I feel the need to note here that before we had dogs I totally judged my friends dogs and I was like "OMG their dog is NOT well trained...they need to do something about that." And even when we got Coby he was already trained and a perfect angel--minus his furious and uncontrollable humping of other dogs-- but now that I have a puppy that we have to train from the ground up...I am sorry for judging!)  It is SO HARD to discipline that adorable little face. One day Otto bit my nipple...hard bite...no bra...and it was sooo painful and grabbed him and slammed him down on his back and yelled at him. But then he gave me little puppy eyes like "Mom why are you mad I thought we were playing" and I felt awful and cuddled him for like 10 minutes. He's also in the habit of making a huge mess of his water bowl and still hasn't quite mastered going to the bathroom outside:

As you can see, I cannot discipline him and he can do no wrong.  This is not boding well for parenthood...though I think it makes a big difference with humans that speak but still I can't imagine myself yelling at a three year old. So we are taking Otto to obedience classes soon (haven't actually signed up yet but found a reasonably priced class right at Petco) and I hope it works!  I am great with positive reinforcement (You peed outside! Here's a treat!) but I don't know how to stop his bad behaviors like barking and dumping out his water bowl on the floor and chewing the couch.  Any suggestions for us in the meantime?