Once you've been cleared by your doctor to start the cycle, you'll take your first dose of clomid on the day your doctor has instructed, taking one dose every day for five days. Your doctor may tell you to take the clomid pills on Cycle Days 3, 4, 5, 6, and 7, or she may tell you to take them on Cycle Days 5, 6, 7, 8, and 9. Some doctors will have you start treatment on Cycle Day 2 or Cycle Day 4, though this is less common.
There doesn't seem to be a difference in pregnancy success between starting clomid on day 3 or day 5, and different doctors prefer to use different protocols. In some cases, your doctor may even ask you to change the day you start treatment on a different cycle, to see if it'll make a difference for you.
You should ideally take the clomid at the same time every day, and some say that taking the pill before bed can help you sleep through some of the side effects. Others do better if they take the pill in the morning. If you have another clomid cycle, you can try taking it at a different time of day, but don't change the time of day once you start the cycle unless you speak to your doctor.