I think I understand you better now. To get accurate concentrations of the analytes in your sample, you will need to get (or make) a calibration standard. All "Area Percent" tells you is what fraction of the total material that provides a response is that component. For instance, if you have 3 components and the chromatogram only shows 3 peaks:
A = 1000 cts
B = 2000 cts
C = 40,000 cts
The total area is 43,000 cts. The %A = 1,000/43,000 x 100 = 2.3%, %B = 2,000/43,000 x 100 = 4.7% and %C = 40,000/43,000 x 100 = 93.0%
If your chromatogram would show your 3 peaks plus something that is unknown, the Area% for your analytes will change because of that additional peak. The concentrations of your analytes might be the same. This scenario doesn't even account for part of your sample that might be invisible to your detector. If your sample has air or a noble gas or CO2 in it, the FID will not respond to them.
You really need a standard of known concentrations of your analytes for good quantitation.