Layer position doesn't necessarily affect the "clickability" of button symbols. As a general rule, what matters is whether or not the button is obscured. For example, if you position a button's layer lower in the stack -- and if doing so places the behind behind some other element -- that might keep the button from working, but even that depends on a couple of factors, including what version of ActionScript you're using and whether or not the asset above (the one that obscures) is also programmed to intercept mouse interaction.
Fortunately, this is easy to test! It's probably a good idea, too, to make a handful of small test-case FLA files that illustrate a particular concept in isolation. Create a new FLA and draw a quick shape. Convert that to a button, then position the button behind another shape in a layer of its own -- in the same layer as the shape -- then convert the shape to a graphic symbol, to a movie clip symbol, to a button symbol ... you get the idea. In short order (say, within 15 minutes) you'll get acclimated and learn how various symbols interact with one another.
> Anyway, I decided to have the buttons move across the screen as
> the page loads. I created a different layer for each button.
Because you're animating these buttons, you did right to put each symbol on its own layer. Given the rest of your design, it may make sense to put those layers above the others, but again, a quick bit of testing will let you know for sure. As a matter of convenience, I recommend you create a layer just for ActionScript, name it something like "code" or "scripts", and position that layer on top of everything else. By having it on top, you'll always know where your programming is (no matter how many layers appear under it), and you won't have to scroll around to find it. You can put all your code in one layer, and have it "reach out" to any other layer (such as your button layers) to communicate with objects in those layers.
Co-author, Foundation Flash CS4 for Designers
"Luck is the residue of good design."