I have separated art into 3 separate layers, Blue is fill, Black is line and Green is fill. However, as you can see in the Preview image everything inside the double lines (Green layer) get filled.
Am I doing something wrong or is this not possible?
Maybe the green lines actually make a closed shape? (a big lozenge-like figure)
You can change the settings to get the fill layers to be actually filled, it might help to detect such problem.