I'm not sure the difference between the methods but I used the one that gave me the least and then went and customized it anyway. I went to a 'bodpod' which measures your muscle mass, baseline metabolism and body fat because I was not losing weight (you can google it for one in your area- about $70). I WAS losing inches however. I see a nutritonist who is also a doc and she recommended it to me.
Turns out I don't burn nearly the calories they gave me ( surprise!) so I customized it.