I always record my temp and the note if there were special conditions: such as a different time, cold room, sick, etc. Missing one temp won't make a big difference. It is better to take your temp at the same time, so if you normal wake up by 5:15am, you could set your alarm for around 5:00am, temp then, and go to sleep.
As for CM, I'm learning that too. This should help:
http://www.fertilityfriend.com/HelpCenter/...y_signs.html#19