I have 2 subs behind my screen wall. As you mention, the screen is AT already, and hopefully any "wall" around the screen is done with acoustical transparent material as well, then you will be fine to put it back there. People do this all the time.
Here is my front speakers and two subs (One large SVS cylinder sub, and my DIY sub that I build to sonically match the SVS.)
Here is the same area with the screen up, and one of the bottom panels (black) in place. On the floor is a frame for one of the sides of the screen with the black AT fabric ready to be attached.