Usually, we recommend taking one pill shortly before the fast begins and the next pill shortly after the fast is over. Since they will both be taken within a twenty-six hour range, they should be effective.
Major changes in pill timing can lead to spotting and reduce effectiveness. Dr. Deena Zimmerman, medical director of our website, recommends gradually adjusting the timing of the pills. If you currently take a pill each morning, you can gradually alter the time in advance, moving about one hour later each day until you are taking a pill in the evening. After the fast, you can gradually move the time back to the morning whenever it is convenient. (You may want to wait until after Yom Kippur.) Since the change in routine may make it more difficult for you to remember to take the pill, you may want to set up some type of reminder (e.g., on your cellphone).
As always, you can avoid becoming niddah from staining by wearing colored underwear and avoiding looking at toilet paper.
If necessary, an unflavored pill (but not one which is sugar coated) can be taken without water on the fast day.