The way I do it, is get the picture being shown on the screen, and then turn the glasses on. I think they have to get a sync signal, which I think only occurs when the PJ is putting out a 3D picture. But it may be that it doesn't matter, and you can do glasses first... I just have a set order I set things up, which seems to work fine.
That's with the 6000W, but it should be the same for the 5900 too.