First, unless you have a faulty thermometer then don't worry about flat temps, or even kinda low post-O temps - if you're not spotting/have a short LP then it's fine and there are plenty of charts in the FF gallery that will have those kinds patterns with a bfp
Second, your temp will start to rise from when you wake - even if you lay there doing nothing, it WILL start to rise. So, in the interests of being as accurate as you can, use the first temp upon waking. I know it's really tempting to put in a temp that makes your chart look prettier but you're either pregnant or you're not - fudging the temps doesn't actually alter that!
Lots of good luck for this cycle!