If you're scanning many frames from the same roll of film, there are several things you can do to maximize the quality and consistency of these scans.
The first thing to do is to compute a fixed exposure for this roll of film (this tells the scanner how long to expose the CCD when scanning the film). If you're scanning negative film, find a frame that has the most clear film in the frame (i.e. the most underexposed frame) and if you're scanning slide film, find a frame that's the most over-exposed. Scan this frame using all-default options (use "File|Default options", set the media type, then use "Scan|Device"), and then turn off the "Options|Auto exposure" option. The values for the RGB exposure (and infrared exposure on Nikon scanners) are the values that should be used for the whole roll.
Without changing anything, now turn off the "Media|Auto mask" option. These three values for red, green, and blue mask should then be used for the whole roll of film.
Regardless of the lighting conditions, shutter speed and aperture of each frame in the roll, you should use these fixed values for exposure and mask for scanning all frames on the roll of film.
Once you have the exposure and mask values fixed, you can scan the whole roll of film with these values. If you're using the same lighting for all the frames on the roll (or a subset of the frame), you can lock the color balance by scanning the brightest frame in the series and then turning off the "Auto black point" and "Auto white point" options. This will lock the black and white points for the scene, and will produce consistent colors for all the frames in the series. This is also useful if you're scanning panoramic scenes that have all been taken with the same lighting, shutter speed and aperture or if you're scanning a series of studio shots taken with the same lighting, shutter speed and aperture.
Another thing you can do to optimize workflow is to scan to raw files and later experiment with color correction. If you turn on the "Files|Output raw file" option, the raw data from the scanner is written to a series of files when scanning. You can later batch-process these raw files by changing the "Device|Scan from" option to "Disk", and set the "Device|Frame numbers" option to 1-N. For instance, if you produce raw files named scan0001.tif, scan0002.tif, ..., scan098.tif, you can re-scan all these files without needing to insert the film again by setting the frame numbers to 1-98 and then using the "Scan|Device" command.
If you're saving raw scan files, you probably will want to turn off the "Files|Output TIFF file" and "Files|Output JPEG file" options. You may also want to capture the entire scan region instead of the auto-cropped region by turning the "Crop|Auto crop" option off and setting the "Crop|Crop size" option to "Maximum".
If you turn off the "Crop|Auto crop" and "Options|Auto exposure" options, then the "Scan|Device" command won't first do a preview scan. This can save time when batch scanning.