Generally even people who sleep in two episodes have one major rhythm that entrains to light. Melatonin doesn't rise that much during the day, no matter when you sleep, for instance.
So usually I would recommend trying to maintain a "dark night" for 9-10 hours even if you are awake for half of it - would probably set your wake time for the "night" sleep episode (i.e. you wake up at 5AM).
As for reducing alertness or reminding yourself to go offline during the day, we don't have anything automatic yet, but you could use the keyboard keys to adjust f.lux if you want to.