I make my maps in Photoshop first, and then feed that to a monitor for my players to copy over onto the battle mat as we're playing.
http://*****.com/ddzxB.jpg
On the board, I have a handful of yellow Alea Tools that we use to mark where the light sources themselves are, and a bunch of square dowel rods cut to the appropriate lengths and marked in the middle to show where the leading edge is.
http://*****.com/PTFgT.jpg
We used to use transparent overlays, but decided that extra layer of crap was more of a hindrance than a help. Then we changed over to 4 yellow markers to mark each corner of a light source; but then you had to move 5 tokens every time you moved a character, and the board was just too cluttered and confusing.
Using the dowel rods to mark the entire pool of light means that we're all just readjusting the same 2 or 3 pieces based off of where the focus is on the battle mat.