I'm editing a new HD (full 1080p) project on FCP 6 and everything is working great so far. BUT the macbook itself is getting super hot, no performance problems but how concerned should I be, and is there a "best practice" for limiting the damage being done?

Mine gets pretty hot too. Keep it elevated so it dissipates heat better. I have the Podium Pad and it works great for this.

MACbook-pros are known for their heating issues. I already had to replace my macbook's fan in its first year. I bought a ILap and I am trying to keep it cool. Running extremely hot just reduces laptop's lifetime. I would say you should try to keep it cool even with a external fan or something.

Postworx designs clip on balls to attach to the bottom of laptops in order to allow the heat to vent from the bottom. You can usually get them at Apple stores. I had a pair for my old powerbook.

Though, I do notice that the Macbook Pro does heat up a lot. Right now, mine is too hot to hold, and all I'm running is Safari, Itunes and Word.