I recently watched the Title Boxing series instructions and they would recommend a workout similar to this. Start out by jabbing only for 1 1/2 minutes single jabbing, doubling it up, and multiple jabs, body and head. After a round of jabbing work on your straight right. Once again single, then multiple. Drop down and shoot some to the body as well. After a 1 1/2 minute round of that, do a round of left hooks. work the head and the body, focusing on form and getting as many punches in as you can. After a 1 1/2 minute round of that, then mix it up with your combinations of all of those punches above. Work hard for a minute and a half, then repeat 1 more round of combination punching, really trying to burn yourself out, but keep correct form at all times. Work on your footwork and movement around the bag, and always keep your proper spacing and balance. Hands up, elbows in and protected just like you would in the ring.
Once you build your endurance up, you can extend your round times to 2 mins, 2 1/2 mins, 3 mins.
Its also recommended that you keep a mouthpiece in while your hitting the bags, so that you really stay used to the difference in breathing with the mouthpiece.
For shadow boxing, you want to work for full 3 minute rounds, and really concentrate on visualizing an opponent. You need to stay disciplined in your footwork and defense, always remebering to keep your hands up, elbows in.
Work on your footwork and balance, moving forward and back, rotating, and really simulating your movement in the ring. Its also a better workout if you shadowbox with gloves on. Its a little harder on the shoulders, and really gives you a nice workout. Focus on practicing proper form, and working on visualizing your punches and combinations.
Hope that helps.