I change the longitude in f.lux's location setting to a location which matches the time of day I'm actually awake. Then I can set the "earliest wake time" to the actual clock-time I want. Fiddly, but IMO it's better than trying to change your computer clock just for f.lux, and works better than trying to juggle other settlings.

(Note, it's 15 degrees of longitude for every hour. West for later, East for earlier. So if your shift is midnight to 8am, and you want to get up just before work, so you're going to bed at, say, 3 or 4pm; then you want to set you longitude around 120 degrees East of your actual location. Ie, LA is 118deg W, so if you live there you'd want to set location to 2deg East. London is zero degrees, so Londoners would set their location to 120deg East. Sydney is 151 deg East, so there you'd set your location to 89deg West. Then set your earliest wake-up to 11pm or whenever you get up.)

This method also makes it easier if your shift rotates. Work out the longitudes that correspond to each shift, just once, and write them down, then adjust as you need. (You might even get clever and use smaller adjustments during the week before your next shift-change to help you start adjusting in advance.)

If you are always on the night shift and sleep right after work (i.e. in the AM):

1. Set your wake time to somewhat before you wake up (2-3 hours before)
2. Use the preset called "working late" so the sunset has no effect on your screen

We are working on better (automatic) solutions for this, but this is my best advice right now.