Ergonomically speaking, a backpack isn't an efficient way to carry a load on a bicycle, because the weight is distributed too high, and you can get a very sweaty back that way.
Going back to one point you made earlier, how did you decide on the best route to use when cycling to work? (check:decide on)
I found the most effective way of finding a good route was to simply go out on my bike on weekends and use the trial-and-error method to find a bike-friendly route.
I should add that it's a good idea to check your fitness level with your physician before you start commuting by bike, especially if you haven't been in the habit of excercizing lately.