I have MFP as well and i think everyone uses it a little differently. if you do log activities, for the most part it does not matter wether you use fitbit or MFP, just dont use both for the same activity because then you could be double dipping. MFP added a 'start time' feature, so theoretically if you tried to log 'jogging at 3.5 miles per hour for 45 minutes at 6 pm' on both devices the integration should cancel one out.
The Goal Zone is an integration component designed to help keep you on course for your daily fitness goals. I dont like it to terribly much because it gives the perception to eat less than 1200 calories per day. it updates based on syncs with the device and manually entered data from other apps. if you ate a big lunch, but planned on going to the gym in the evening the goal it would likely show you being over your 'calorie budget' for the day. once you hit the gym, it would correct itself because theres physical activity that made a negative caloric impact on the foods you ate. make sense?
Personally, i use MFP for FOOD only and fitbit for everything else. occasionally- when i want to track weights lifted i use the strength exercises section but that doesnt track any caloric burn.
if you are really trying to lose weight above anything else I recommend a hand written chart (i use a note book page) write the date on each line, and then make columns for: calories consumed (taken from MFP), calories burned (taken from fitbit dashboard) and a +/- column (for the difference). at the end of the week you can see what you 'should have lost or gained' based on calories alone.
i know its long winded- but i hope it helps! Best of Luck.
