I live in a place where I get to see and film sunrises over the Cascade mountains, and I like to make timelapse movies of those sunrises. After a lot of experimentation I have found that setting the meter exposure down two notches really helps to capture the color. I set the aperture somewhere between F22 and F16 depending on the lense, the light and how wide of the shot. Then I set ISO and shutter speed on auto. This combination has given me some decent results. Of course you want the most sturdy tripod you can get.
At first I tried not using auto anything and just tried to keep up with the changing light. This did not work near as well as my current method and required a lot more attention. There was always a lot of shake in the shot sequences and the light adjustments were typically obvious (unlike with the auto settings). Light is changing so fast at sunrise that it really is hard to keep up with, the camera's computer does it much better and faster than I can -- but you have to be sure to set up the conditions so the computer is working to help you. That might take some trial and error before learning how your camera deals with this situation.
I am no pro, but I think the 'old keep it simple' axiom is always a good idea. My timelapse work has been looking a lot better since employing this method.