This is a difficult question
the value/effect of layers depend entirely on what you want of your web page, and what you have to display
so you decide the best way
the w3 z-index tutorial is a start
layers work only of fixed objects
its one way of fitting more than a screen full of information without scrolling.
a top layer of 1pxtransparent.gif makes it harder to right click copy your images, they can copy but they get the upper layer
layers of images can be used to highlight important sections onclick or onmouseover.
with transparency, show/hide, move to front, send to
its a tool
Flash-like effects without the overhead