Ceomgenus,
Your inquery indicates that it would help if you could get someone to take you through the basics on the GC. I don't see a strong emphasis on GC in anything that Case Western offers in the chemistry classes - but look around for a lab where someone is using GC and is willing to talk with you. Some of the things you need to know can be found in books and some just get passed from senior to junior. (And the trick to learning GC from a book is realizing which parts are not important at the start.)
If there is no one around at Case Western, then you could look across town to Cleveland State. They list that they cover GC in the analytical chemistry classes, so there may be someone there to talk to.
On the question of two peaks from methane - we would have to go back to the source of your methane and then your sample introduction method (syringe, sampling loop, etc.) and the possibilities continue.
Actually you want the FID temperature to be high enough that you do not get condensation or fouling. (The manual should have reccomended set points.) And, it is rather unlikely that you would form Hydrocarbons in a flame - and even if you did this would all be at the time that the chroamtographic peak is emerging - it would not form a separate peak, as the compunds are separated in the GC column. In a proper FID flame all methane should be turned into CO2 and water. (OK, I have made soot in an FID flame, but you have to push it...)
How much methane went past the FID... That is why we build calibration curves. Hou have to inject some known levels of methane and then you can use areas to calculate quantity.
Good luck.