My advice would be to keep your wake-up time set at 7 am, and not use the sleep-in option. If you sleep later than that sometimes, it doesn't matter. Yes, it means your screen will be rather orange after 11 pm, but that's exactly what you want. For the most part, it doesn't interfere with using the computer. If it's really too orange, you can change your Bedtime setting to a higher colour temperature, and compensate by turning down the brightness of your screen - which you should do anyway at night. There's also Movie Mode, again you should dim the screen as much as possible if you use it at night.
Other than that, f.lux isn't designed to have its timing adjusted on a daily basis - and neither is your body. F.lux helps keep your body's internal clock in sync with the clock on the wall.
There are two basic things that make you sleep. One is your circadian rhythm, your body's clock, that causes you to sleep and wake up around the same time every day. The other is whether you've had enough sleep overall.
When you stay up late, you may sleep in the next day to compensate. Or you may have a nap in the afternoon, or go to sleep earlier than usual. Your body keeps a kind of running total of how much sleep you've had in the last few days, and will try to compensate for a deficit when it can. It doesn't necessarily change your body's 24-hour clock though. That gets synchronized to local time mainly by exposure to light, but also by temperature changes, meal times, physical activity, and so on.
The point is that if you stay up late, you may feel tired the next day, but you can get over it and get back to your regular schedule fairly quickly. But if you stay up late and expose yourself to white or blue-green light, you're actually moving your body's clock forwards. You end up with a case of jet-lag, and it's more difficult to readjust during the week.
Think of it this way: if you stay up three hours late one night, you don't go around the house setting all the clocks ahead. You shouldn't do that with f.lux either.