To be honest, I don't use it and I don't care for it. It's only there because some people wanted it for certain things, and Mike and Lorna (the f.lux team) felt it was worth adding and so they added it. You don't have to use it just because it's there. Hell, I don't even use any of the automatic settings. I keep all 3 color temperature modes set to 800K, and so when I want 800K I just launch f.lux. I don't even allow f.lux to start with Windows. I use probably 5% of the program's abilities, but I'm one of the biggest fans.
So, just use what makes sense to you to use and call it good.