I have a fitbit and you're right - because it adds up all your active minutes it does tend to go super crazy with the minutes and calories. The sync was an excellent idea in theory but in practice it doesn't really work does it? Maybe if they only moved over your most active category of minutes it would be better but we must work with what we're given, huh?
I do a 45 minute session on the elliptical every day and set a timer on my fitbit so I can create an activity log. I then input this as 45 minutes on the elliptical on the SP tracker and do not sync my fitbit.
When I go for a walk or run, I also set another timer on the fitbit so I can track my distance and time. I then input this manually as mileage on the SP fitness tracker. So in short, I let fitbit sync with sparkpeople for the food side of things (fitbit knows better than sparkpeople does how much I have been moving around so the daily calorie totals are more accurate) but I do not sync the fitbit with spark, preferring the accuracy of inputting the data myself.
I love my fitbit though, it's amazing!