Hey shez - I think dragontail would be best to answer your question cuz she is bbt expert.
What I did before was to use the later temp. But I put a note that I had an earlier temp too. Why I took later temp - same circumstances as you - the first time I woke up I stared at ceiling for a while before taking temp and so body already had time to warm up and hence temp not accurate. The second temp given I woke up 4 hours later was taken immediately when my eyes opened so I figured that was more accurate.
But that was just my own analysis. Not sure if it "holds any water".