I had this question when I started using f.lux, and it took me a while to figure out. It comes up regularly on the forum, so I'll try to make a good answer to point people to in the future.
Until new f.lux versions come out, you have these options for manual settings:
From the f.lux menu, choose "Options: Expanded daytime settings" and make sure it's checked. Then you'll be able to open f.lux's Preferences and drag the slider, to manually set a lower colour temperature at any time of the day. If you want your screen to stay a constant colour all the time, set the Daytime, Sunset, and Bedtime colours all the same.
Note that if you lower your daytime setting, it may also lower the sunset and bedtime settings too. But when you raise the daytime setting again, it won't raise the others. So you might have to do some adjusting to set things back the way they were, or just choose "Recommended Colors" from the menu to reset to the defaults.
Setting the time of the automatic Daytime-->Sunset transition can be done by changing your location setting. The closer to the Equator you set it, the more stable the sunset time will be as the seasons change. You can adjust what time it happens by moving farther east or west.
Setting the time of the automatic Sunset-->Bedtime transition can by done by adding eight hours to your desired bedtime, and setting that as your wake time. It doesn't really matter if you don't actually wake up at your wake time. But if you're working in the morning when the sun is up, and your screen is still tinted, choose "Disable: for an hour".
Remember that the overall brightness of the screen is important, so you should manually dim it at night, in addition to changing the colour temperature with f.lux. Also dim or turn off your room lights.
If you change f.lux's Preferences panel often, you can set a hotkey or trackpad gesture to open it - see How to create keyboard shortcuts. However, you may find that there's less need to manually adjust things than you might think.
F.lux is designed to help avoid artificial light at night, especially blue light. If you're working late, try to resist adjusting your bedtime colour or your screen brightness higher, or your bed/wake time later, even for one night. It will affect your body's circadian rhythm more than just staying up late does, and make it harder to wake up and fall asleep on the following days - basically it will give you a case of jetlag.
Light in the late afternoon and early evening has little effect on circadian rhythm. The later it gets, the more sensitive you become to light. That's why f.lux gradually reduces blue light during the evening. The aim is to never be exposed to an amount of light that will negatively impact your natural body clock. If you decide to go to sleep early, it shouldn't be necessary to reduce your screen's colour temperature earlier than usual, if you have it set up correctly. You can just go to bed.
In other words, bright blue light in the evening artificially keeps you awake and changes your body clock. But dim orange light doesn't artificially make you sleepy - it doesn't do much of anything.
