I was confused about this when I first started as well!
Lets take the Achievement window for instance.(under Source.Gui)
Open achievement.fla. Look at your timeline, you should see a little "a" in the as layer. You can right click that, and goto Actions(should be last option). It will open the actions window and now you will see "#include 'achievement.as' "
Ok so now we have the base AS file for the achievement window.
NOW look in your library and find AchievementWindow. Right click and goto properties, you will notice an Identifier "AchievementWindow" and your class "GUI.Achievement.AchievementWindow". It is referencing your AchievementWindow.as (which is just a class AS)