What I do is, I just delete the f.lux entry in the Registry that makes it start with Windows. This way, I simply launch f.lux when I want f.lux. I'd like to tell you where the key is, but I'm sure that's best kept to private messages.
I keep all 3 f.lux modes set to 800K so that I get 800K regardless of when I launch f.lux. I require a melatonin supplement (3mg) to sleep properly, and so this works perfectly.
So, when I know I will want to be sleeping in 2-3 hours, I lower my monitor's brightness all the way and then I launch f.lux (or I launch f.lux first, it doesn't matter). I also change all my indoor lighting to blue-free light (red and orange/amber). Then, about 10-15 minutes before going to bed, I take my melatonin and then I'm all set.
With the way I do it, I don't need a scheduler or anything like that.
So yeah, I bypass all of f.lux's automatic operations completely.