I'm not qualified to say exactly what they do and why... I'll leave that to ICDP or one of the painters that actually understands and can explain without mudding it up. In laymans terms, here is what I've figured out:
Alpha layer is about reflection. I'll be specific to the P-51, but this will work for the B-17 etc. If you have a painted surface it will reflect less than the bare metal. In the alpha channel you are working in black and white. White= Less reflective, Black= something out of the terminator movie. You can look in the paintkit and see that the paint, titanium, and bare metal layers get progressively darker. In general I use the paintkit settings for the default parts and then copy all of the graphics I've painted and fill them with 235,235,235 white. This way they don't look chrome, but I can still see where they are in my file. I should also note that you can accent detail in this layer, but it does not display detail (Assumption based on experience) So in this layer your nicely detailed nose art is just a white blob that has the same outline.
Ok now that you've told which parts should be shiny and dull, you open the Spec file. This file tells it what you want it to add to your base colors when the sun hits it. This is why the metal is blueish in that file. It adds in that aura to the grey in the base file. In the P-51 the spec files are half the size. I'm lazy and make a copy of my main paint file, open the file, resize it down to 2048x2048, drag the full detail nose art layers into my spec file and then delete the copy of the smaller original. You now have your clean colorful noseart in the spec file with the blue metal background. In the sun, this would wash out a bit, so I reduce the fill and opacity on the nose art to something like 75%.
Spec alpha is the final piece to the puzzle. This tells it the intensity of the reflection. Does it look like glass and washout everything completely? or does it just look like a pinpoint of sun on a paintchip. Again use the paintkit as your guide. My method on this changes with almost every paint, but the rules from the alpha later apply. Blobs not detail. If you ever forget, look at the us star insignias in the paint kit. You see detail in the base and spec, but just the outline in the Alpha and spec alpha.
So in any repaint you have 4 files that combine to make 2 files. I paint everything once in the base layer, and then copy that work into the other 3 psd files (sized appropriately) and make them work for that particular file. If we had to paint everything 4 times this already long process would be insane.
I hope this helps a bit. Like TJ said in another post, this is all about trial and error and patience. I learned about alpha and spec files from an ICDP/Jankees exchange in the P-47 thread. From there I started playing with it, and have gotten a bit more comfortable with each paint.
Good luck! As always, we are all here to help. Keep asking questions, and you'll get as many different answers, but your method of choice will be in there somewhere.
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I have been trying for a while now, and cant even get a natural metal look....just grey 
