Ngala
If you wake at 5.30am on weekdays then I would be setting the alarm for 5.30am on weekends as well. It is important to try and take your temp at the same time everyday if at all possible. Otherwise you get a yo-yo effect and it makes it really hard to track what is happening.

I got into the habit of taking my temperature when I was 3/4s asleep after awhile. My thermometer beeped at me to take it out, and often I wouldn't even open my eyes but just chuck it on the bedside table and read it later on when I woke up properly.

That said, there are two phases of your cycle that you are going to want maximum accuracy - around ovulation and around the end of your cycle. In between you can slacken off.

Renee is also completely correct about the 3hours sleep thing. On my last cycle before I was sure I was getting AF because my temp dropped dramatically -- but I also had a terrible night sleep when I never got more than 3 hours consecutive sleep. In fact the low temp was an artefact of the broken sleep because 3 days later I got a BFP and my real temps were sky high.