Ideally, you will be able to take your temperature at both the same time and after at least three hours of sleep, but sometimes this is not possible. Do your best to meet the ideal as closely as possible. Whether or not you will have a more accurate temperature after sleeping the longest or at your usual wake-up time varies depending on your own unique metabolism. You will only really know after you have charted for several cycles and have experimented a little bit.
Fertility Friend can usually make sense of your chart pattern even with a few less reliable temperature points. When basal body temperatures may be affected by your sleeping and waking pattern, it's a good idea to make note of the circumstances. Also, play close attention to your other fertility signs for cross-checking.