I can confirm the above post that says you can mark the lightwell. You can target it, you just don't have to.
My guild is benching 25 mans until Cata, but my 10 man has gotten very used to clicking it, very quickly. I tell them ahead of time when I'm going to set it down, and use one of the built in raid flares to mark where. Then I say on vent that's it down, and to my complete joy, they actually clicked it.
It's pretty nice, really.