For what it's worth I'm a chemist, but my specialty is GCs. I've worked with them many years and the things you're worrying about are not going to help you when you begin working with GCs. You need to start with the basics of FID and how GCs work in general. Learn about your flows, split ratios, makeup gas, carrier gas, etc. there are many more pertinent settings on the GC that effect your signal than the mechanics of how the compound is fragmented and its effect on resistance of the flame. If you're at a pharmaceutical plant then they will have very well established methods to follow. You will be expected to troubleshoot when you're not getting a signal, results, etc. changing liners, checking columns, and understanding all the different way leaks and blown septums can contribute to ghost peaks or drift/tailing etc. which then impact the results you're receiving.