The new full-screen function isn't usable for multiple monitors/displays whatsoever. The function simply isn't built to use a single display for separate spaces and full-screen application. I encountered this with trying to watch full-screen videos in Quicktime on my second monitor while trying to do work on my main monitor. It just doesn't work. OS X Lion totally ignores users with multiple displays.
This is the single reason why I am still using Snow Leopard on my iMac which has two additional displays connected to its ThunderBolt ports.
I didn't buy monitors to display fake grey linen. The real linen is cheaper.
Please provide feedback on this design decision via -http://www.apple.com/feedback/macosx.html
I'm hoping that if enough pressure is built up, they'll add an option:-
"Allow me to use my external displays = Yes/No"
I use Aperture, and here is what it looks like under Snow Leopard
When running Lion, the left and right screens look like this