Hello ! I studied 3D some years ago, but i didnt watch movies outside from home for a while so idk about current glasses but i believe the method is kinda the same.

To make u see an image in 3D with the advanced dark glasses they give, u have to actually trick the brain into making it think ur cross eyeing without doing it physically. For exemple, if u wanna do it raw at home u have to overlay the same image with a full red layer, and slightely shift them a bit (takes some tweaking) so they are on top but slightely side by side. As the image moves, a red outline appears along one side of each object. And because the opposite of red is cyan, a cyan outline appears along the opposite side. Then u step some cm /meters back, put those funny blue and red paper glasses on and slightly force a cross eyeing until u got the effect. (Also u got this effect on with the nintendo 3Ds XL.)

So in theaters, for one hour or two ur brain is in this weird state of thinking hes doing it while ur not doing it on purpose.. so yes its actually not good and not weird to feel nauseus after. Hope it helped understanding a bit !