How to draw a polygon with clear spaces inside in EAGLE
Draw a 'Cut-out' polygon. Basically this says everything between the cutout polygon and a polygon outside of it should be filled. Everything inside the cutout will not be filled.

When drawing the polygon there  is a symbol on the top bar which looks like a filled box with an empty polygon space inside. Alternatively if you go into the properties you can change the type.



An example of a cutout polygon: