From my recent observation, I have concluded my wake time in f.lux (not actual) should be based on when I want f.lux to activate... for me, that's 3 hours before bedtime.
If your bedtime is 2 am and you want f.lux to activate 2 hours before (i.e., midnight), then set your wake time at 9 am. If your bedtime is 2 am and you want f.lux to activate 3 hours before, then set your wake time at 8 am.
That said, as a fellow sufferer of insomnia, my strategy is to get my circadian clock back on track. That means ALL blue lights off 3 hours before my desired bedtime (even if I wake up at 3 am). I fear you may be unintentionally adding fuel to the fire and strongly advise against that. Google is loaded with root causes and advice on how to cure the annoyance... it goes way beyond our electronics. F.lux has been a huge help to me but I'm still struggling. Good luck!