I want to render a specific layer only between 0-12km but have no idea how to set it in QGIS because the scales dimensions are high numbers. My project and layers CRS is EPSG:2039.
I am not sure what the default is but this should help you set it to KM.
"To set project properties click "[Settings > Project Properties]" in the main menu. The "Project Properties" window will appear. Click on the "[General]" tab and set Project Title and Map Units."
The default for EPSG:2039 is meters (see http://spatialreference.org/ref/epsg/2039/html/) so you'll need to divide the scale denominator by 1000 for Km.