We've just built a set up for our auditorium. There are many options, but capturing video with clear audio in a large auditorium moves beyond more conventional Skype certified devices. It's also not very cheap.
Vaddio make a great range of cameras and audio devices, ending in the AV bridge range that can output USB2 into your broadcast machine. you'll be able to do pretty much anything you can imagine, but the cost start above $5000 for even the most basic setup. Sadly we couldn't get the funding for this.
The other recommended product is to keep things as HDMI and then use a Magewell hdmi capture card like this
http://www.magewell.com/usb-capture-hdmi. Our auditorium has an Extron AV amp that controls the projector, speakers and mic inputs. We take a second hdmi output from this to provide us with what's being projected and mic pickups. We found that without slides our broadcast were unpopular, and no one was ever organised enough to give us content prior to presentation.
It would have been nice to mix together this feed with a camera using something like the Roland V-1HD before the Magewell, but again the costs of a decent HDMI camera were beyond our budget.
Instead we use a Logitech PTZ Pro camera for the video, then use the ManyCam app to mix together the camera and screen feeds into Skype. It works ok, but the IT knowledge to make it all work is pretty high.
