Mise-en-scene refers to the arrangement f the contents in a film frame i.e. lighting, setting and props, positioning of characters and objects, facial expressions and body language, costume, hair and make-up etc. everything you see in a film is there for a reason.
Mise-en-scene can be considered, at a deeper level, a way of considering complex meanings which are open to different readings for example in Apocalypto some of the tribe members (in the scene where the head rolls down the stairs) are covered in coloured paint and wear jade stone earrings. This is to show that they are a higher class of people compared to the rest of the tribe.
As a director you have control over this, some bits maybe written in the script already but it is up to the director for the overall look of the film. When it comes to directing your own film what deeper level meanings can you show to an audience?