I just went to the Natural History museum yesterday to check out their indoor butterfly exhibit. It's pretty amazing first off, and I brought my camera, macro lens and flash along(10d with canon 100mm Macro not that it should really matter).
It's a difficult place to shoot though as they don't allow tripods. Fortunately, it's pretty darn bright in there. Under their hot lights, shooting without flash is definitely doable on a reasonable ISO setting, but move a few feet away and your lighting is completely different....
This was my first butterfly outing, so most of my shots were totally unusable(mostly not in focus). I think I might get better results with manual focusing and moving the camera in and out to set the focus...
I'm no expert but this is basically what i'd do...
Its pretty much on the lines of manual focusing and moving the camera in and out for focus as you said. I'd also set my camera to AV mode and dial in the appropriate f/stop for a good shutter speed pref f7-8 because of the distance from the object being shot and nice dof and Bokeh you`d get. Use the lowest iso setting you can but keep in mind that a good noise reduction will help you out no end in post pro if you have to dial in a high iso setting, shoot raw...
I'd also be very aware of were the lights falling on and around the subject and move you view point accordingly, dont just shoot willy nilly ....
Btw i can't wait to see what results you can come up with...