I just made the leap from car to a bike to get to work. I was nervous about the timing, since I have to be at work by a certain time. What I did was packed up my stuff onto my bike (i have panniers, 'cuz i have a camelbak for water), then did a few test runs on the weekend. It really helped to learn the route before the actual first time in, so I knew where I'd have some trouble.

You might also want to go around the time you'd be riding in to see what the traffic is really like on the road you're taking. On my commute, traffic home at 5 pm is much heavier (and scarier) than at 6 pm.

There was also a tip listed earlier on this thread - it's good to get to where you want to be a 1/2 hour earlier so you can shower/wet wipe down and get your gear situated.

Bags are a preference - I have back issues, so I don't want to load up a back pack and put more stress on it. Again, this is where a test run might help with the gear you expect to use. Start with what you have and go from there.