It doesn’t matter. You just need to make sure that both layers have a background, otherwise the image will be transparent in AI. So you have 2 layers (A, B). Both layers have the artwork AND below the artwork a rectangle which is the same size as the canvas.
Export.
In AE import the AI file, and turn both layer into a 3D layer. Make sure one of them is offest by 1 in the Z direction. You can then adjust the transformation/rotation of each layer in 3D space.
Then you put this comp into another comp, add a camera, and there’s your page that you can rotate in 3D space or move the camera around.
Also, if you are talking about scanning, shouldn’t you be using PS as opposed to AI? Not that it matters too much, but still…