The help menu has some good information, but maybe not easy for a complete beginner.
Basics:
You first need to have the target analytes in the quantatitation database. Best way to start that is to run a mid or high level standard so all your peaks are there and easy to find. In Data Analysis use the Initial Calibration menu and SetUp Quantitation. Here you can setup your default items like peak retention time reference window widths, integrate by area or height, curve fit type, units of concentration and internal standard concentration if you use one. The checkbox for Use RTEINT allows you to select the older style RTE integration parameters which I think work pretty well for MS work, but you may wish to experiment with this for the FID work.
Select OK there and it will take you to a screen where you can setup your compounds for quantitation. It will give you your current chromatogram and a box in the lower right to enter compound information. If you click on a peak it will put in the retention time, you add name and if it is MS data you can do the normal double left click to pull up the spectra then place the cursor over a mass peak and click both mouse buttons at the same time and it will enter that mass into the list. Pretty easy way to setup your list especially if you have a lot of targets.
Once you are finished setting up you can enter your calibration points through the same Initial Calibration menu by selecting the "Update Levels" item. Just select your standards in order, use "Calculate/Generate Report" from the Quantitate menu(you can see the integration of each analyte using the QEdit item in the Quant menu), then follow the next part with each standard in turn. Select "Add new level" checkbox on the popup and enter "level ID" "internal standard concentration"(if needed) and "level concentration". This will give all compounds the same concentration, but once you click "Update" at the bottom it will take you to the edit screen where you can go through each compound and set individual concentrations if you need to. Oh one other point, Chemstation needs the Internal Standard for a group of analytes entered before those analytes, so put your internal standard in before the other analytes. If you have two internal standards you must put in the first, then everything quanted on it then the second internal standard and everything quantated by it, ect.
After you have all your levels entered in you can review them and adjust curve fit if needed in the Edit Compounds menu.
To quantitate your samples, just load them and Quantitate from the menu. To edit just the QEdit option as needed.
In QEdit you can manually integrate by using the right mouse button and clicking and drag to draw the line for where you want the baseline.
Overall pretty simple, and after a little practice you can do it in your sleep.
