Because you haven't clearly described what you are trying to do, in this or your other thread, it's quite difficult for any of us to make any educated suggestions. If you provide some meaningful requirements we may be able to offer possible solutions.
Overall, it sounds like you may simply be expecting too much from After Effect's 3D capabilities. Your requirements may be better met by a genuine 3D application.
No way. They are 2D effects and that is just that. Any clipping and Z-ordering will have to be created using suitable masking and layer stacking.
"All i want to do is place a visible light inside a box shape object made of 3d layers then precompose it"
How much clearer do you want it. Theres only so many words one can use to try and explain what one is doing.
AE's 3D systems do have some limitations. It is not a full blown 3D modeler. I have never really dived deeply into why lights don't flatten/collapse as expected; I just accepted it a long time ago and forgot about it. I place all of my lights in the master comp. Sorry, best I can do for you.
You might try some of the more highly advanced AE tutorial sites. some of those people have been breaking through AE's 3D limitations for several years. Good luck and, hey, if you figure it out, drop back and tell us what you did.