Sure, you could possibly build a huge 3D comp, but that won't do you any good if it doesn't render. That aside you'd need to match perspective still and whatnot, so ultimately it becomes unmanageble. Plan your shots properly and do them separately. Despite extensive copy&paste it will be much simpler.
So the layout is simple, in all the sides of the box are screens, just normal computer screens. in which we make animations in a 3d envoirment. Butttt.. I want to make this in After effects, and i want to make 1 video in a project, but how do i need to make this as an project, i have 5 screes for each side exept the one you look in, but the transistions need to be fluently in the box.
There's never anything simple about 3D.
If I understand, you are going to build a cube with 5 sides and each side will be, as you seem to be saying, a flat 2D movie, "just normal computer screens." You're going to build a script with carefully timed hooks at each point you need something to happen and you are going to build five comps that all follow the same script, exactly to the frame. Then you will render these five movies separately and bring them into a 3D comp. There you will build your cube and fly your camera around.
If you are attempting to build 5 3D scenes that collapse neatly into a cube your'e in for a bit of a shock.
This can be simulated easily if you build the flat 2D movies and then, in your 3D comp you can add foreground elements that will appear to be in front of the flat screens. These will add significantly to the illusion especially if you add some lights that cast shadows. For instance, let's say the back panel of the box is a skyscape some nice clouds and a rainbow. You could then, when you build the 3D comp, add an airplane to the foreground that moves across the interior of the box.