I’m not quite sure what you mean 
after all it’s a box and the normals of a box are usually perpendicular to the respective face (except you’ve been editing the normals ^^). This would mean that you’re always having one face with its normal pointing inwards and one pointing outwards per box. Maybe you could add a picture so its easier to understand what your problem is 
In the end you’re just blocking out your level with BSP’s and model your final mesh with max