I used to reference the following back when I was poking around with ifly.  The concepts are basically the same, though the ifly may be slightly more difficult to handle as compared to the PMDG since it doesn't readily give you some of the numbers you need to input:

http://smithplanet.com/fs2004/pmdg/

I'd also reference some youtube videos and look up tutorials with regards to the PMDG or iFly if available to understand the operations of the FMC.  In general, both the iFly and the PMDG should offer the same functionality (though the iFly may at times feel 'off' or buggy compared to the payware product that is PMDG). 

Not sure if this helps, but basically, the FMC is like a little mini computer/calculator that helps guide you on your way from point A to point B.  It requires you to input at least your position (so it can find where you are), how much you weigh, how much fuel you have for reserve (extra fuel), your flight plan route, and your height. 

If it asks you for an IRS position, you may need to hit shift+z in FSX to determine that (I can't remember if the iFly offers a GPS position).  If it asks you for your gross weight, you can find that in the FSX weight and balance settings. 

I know this is really just skimming the surface, but I think the best way to learn is to just read up on a full flight tutorial of either the PMDG 747 or the iFly PMDG, and try to mimic the steps the best you can.  Once you get flying, the pieces start coming together and you will understand the FMC that much more.  It's really easy to use once you get the hang of it.