I used to say, it's okay for f.lux's wake time to be "wrong" - just set your f.lux time to the earliest time you wake up. But now with the "waking up" notifications we should do a little better, or I guess you should turn them off until we do (options > backwards alarm clock).
Unless you're doing shift work, most people actually don't want to move their circadian timing around, they just want to sleep a little later some days. (Your internal clock takes weeks to adjust, so it's hard to mess with--but the main thing it responds to is changes in light timing.)
Do you stay up a lot later on your late days, or just sleep in later?