I can't say for sure what formula FitDay uses, but I can relate to the frustration of "how well does anyone know, really." Our body knows for sure and anything else is just a guess.
The longer you follow whatever eating/exercising program you do, and the longer you log, you will get more of a sense of how accurate your numbers here are. There are ways to make adjustments. Some of us find it's more accurate if we log our sleep hours, even though that's theoretically taken into account. You can also customize your metabolic rate and put in the number of calories you think you burn through that.
A year or so ago I did one of those hydrostatic body composition tests and part of the result entailed a printout of the calories burned for basal metabolism. I plugged that value into the customized blank in FitDay. If you have anything like that, or data from a BodyBugg or similar device, that's probably the most accurate you can get, but most of the time it's just a "best guess" anyway.
"If you drop an egg, you don't say, 'Oh, shoot' and drop the other 11, do you?"
-Source unknown, but obviously brilliant
Reached goal 4/16/2010...but kind of afraid to look these days