White Balance. Ensure the white balance is also set to manual. Your shooting location and time of day will determine your white balance. Although it's not 100% important to nail your white balance when shooting RAW, it's good to get in the habit of setting it. As a point of reference, daylight is ~5600K and tungsten is ~3200K. When shooting astro time-lapses, I tend to lean closer to 3200K, but I highly recommend taking a few test shots to see what you like best.
How Much Is Important. Once you've set all the internal settings on the camera, you'll need to determine what you want your aperture to be. Most lenses have a sweet spot, and I highly recommend testing out its full range of apertures to find out where the sharpest point of your lens is. When choosing what aperture to use, this will depend on what you're shooting. Keep in mind that you'll introduce flicker if you have your lens stopped down unless you use the "lens-twist method" to lock out your aperture blades. If you want to drag your exposure during the day, I recommend using ND filters rather than stopping your lens down completely. If shooting astro time-lapses, you'll more than likely want to shoot wide open.
Smooth Like Silk. One of the last settings to determine is shutter speed. Set your desired shutter speed based on the effect you want. The longer the exposure, the smoother the motion of the action in your scene. By dragging your shutter (shutter open longer), you're able to hide exposure changes, and as a result, remove some of the flicker that would have been present otherwise. Usually, I wouldn't recommend a shutter speed faster than 1⁄100 sec., as you'll start to see more flicker from changes in light within your frame.
If trying to drag your shutter during the day, you may want or need to use an ND or a polarizer filter to get the desired shutter speed. By dragging your shutter, you're creating motion blur, and as a result, you're creating an image similar to shooting video at 24/25 fps. However, if you want to create a "stop-motion" effect, you may need a faster shutter to freeze the action within the frame.