I think you have 2 options. You can take your temp on the way to your dc, or you can wait and take it in an hour or 2 when you are up for the day. Personally, I've been obsessive about taking my temp to see how much it changes from waking to pee at night, to waking an hour or 2 later in the AM, to what the difference is when I get out of bed. (its been like a science experiment :LOL ) And I've found that for me, its OK to take the temp as I'm moving around a little- it doesn't raise it that much for me, and I can still tell when I O. So if it were me, I'd take the temp as you get up with dc, stick the thermometer in your mouth on the way to his room, and record it before you go back to sleep.
However, it is best to relie strongly on your CM when you are just a little erradic in your temp times. Good luck!
Laura, Mama to Mya 7/02, Ian 6/07 and Anna 8/09