Part of teaching Marlin that you are the boss is start wherever you can. It may sound weird to do these things that are not related, but overall, Marlin will start to get the message that you are boss. No need for punishing or negative reinforcement. Here's a start. For one, start having him earn everything. If he wants a treat, make him sit (or anything like lie down, speak, sit up, etc). If he want to be petted, ask him to do something first. Marlin follows the command, he gets what he wants. Make him sit before you put his food down. You get the idea - he has to earn what he wants.

My collie has a habit sometimes of barking to wake me up, too. But he has learned that until he lies down and is quiet, I won't get up. So at first you may have to sit up in bed and tell him to lie down. As soon as he lies down, immediately jump up and give him what he wants. This is very important because you are retraining him. Do it again and again until he gets the idea. As soon as he's figured out that lying down will get you up, you can start increasing the time between when he lies down and when you get up. With my collie, he will come lie next to the bed patiently now until I get up. Sometimes he will be try barking again, but for the most part he is a patient boy now.

Here is some more stuff about being the boss: http://loveyourdog.com/boss.html

Good luck!