Thanks for your question.
You simply need to tell ACE to "Fill Closed Polylines (FCB)" and then create composite layers (i.e. assign Dark/Clear areas for islands and holes within a polygon), please refer to the composite section of EasyGerb Help Manual.
Here's a tutorial movie (no sound showing the exact steps to take):
Note: For example on the Top layer, all you need to do is put entities that will be "Clear" (i.e. Hole) on a separate layer called "TopClear1" (or whatever you want to call it), and if there are additional islands (i.e. dark areas) that go inside the the TopClear1 layer, then create another layer called "TopDark2", etc. The when starting EasyGerb, press the button "Merge Layers".
Note: We have many other examples in the EasyGerb user forum discussing composite merging. When starting EasyGerb you should see a box called "Ask A Question". Simply type composite and press enter - you will instantly see all DXF