Guidelines from FF:
1. Take your temperature just as you wake up in the morning, before doing anything else.
2. Take your temperature at the same time every morning, or as close to the same time as possible.
3. Take your temperature after a solid few hours of sleep.
4. Take your temperature using a special BBT thermometer.
5. Enter your data on your chart or bedside notepad as soon after taking your temperature as possible.
Is it important for it to be at same time or after three hours?
"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."
It's important not to talk, drink, eat, walk around, etc. before taking temp as that may affect it. Waking up at different times can make a big difference for some people and some people say they do not notice much of a difference. There are those who support adjusting temps when they are late and many who really disapprove of doing so. I'd say try to take it at the same time every day.
Your temps before ovulation will be lower and then they will shift to a higher level after ovulation. The websites below are good for tracking this for you and will determine when you have ovulated. I'd suggest monitoring your cm as well because that will help you determine when you might be ovulating. Opks should tell you in advance as well. Temping is great for confirming that ovulation did happen, but opks and monitoring cm should tell you before it happens.
A couple of good charting sites that you can use to track it and that provide more information and articles:
fertilityfriend.com
ovufriend.com
Good luck!