I shot a day into night time lapse for one of our energy clients a few months ago. In this instance, the camera was facing west, directly into the setting sun. I wanted the shot to go from full day light to full nighttime with the lights of the city in the shot.
I set the camera to shoot one frame every 8 seconds (iirc). I always shoot everything on manual. Our camera, a Sony XDHD camera, has built in neutral density filters so I dialed in a four stop ND filter, set the aperture to the correct exposure (probably f/11 but I didn't take notes so I'm just guessing) and waited. The shutter speed was set to normal (about 1/30 sec and never adjusted)
As the sun dipped lower, naturally the ambient light grew dimmer so I would manually open the aperture just a fraction. I used the 70% indicator in the viewfinder as an exposure indicator so whenever the "zebras" in the viewfinder started to dip, I would open up the iris to keep the zebras in the viewfinder approximately the same. (to those who have no clue what "zebras" are, it's a series of alternating lines in the viewfinder of a video camera that indicate skin tone, or 70% of white level-kind of like the histogram on a still camera)
Once the sun dipped low, I had to dial out the ND filter. I would do this quickly and reset my aperture to compensate for the sudden increase in light. During editing, we would edit out the few overexposed frames. Once the sun was completely over the horizon, I had to start dialing in some gain. Basically this is the reverse procedure as I did for the ND filters. I'd add gain, then stop down the aperture to compensate to keep the exposure constant.
At the end of the shoot, I had gone from 4 stop ND filter with my aperture set around f/11 to +20db gain and my aperture wide open, all done manually in 1/8 stop increments.
It made for a beautiful sequence.