Seperate Signal Planes in Eagle
Give each one a seperate rank (found in the properties dialogue). The lower the number the higher the priority. So a polygon of rank 1 will be drawn first, then ones with a rank of 2 will be drawn next (being cut away by the higher priority polygon outlines).

This will allow you to have polygons inside polygons.



The second part of your question, if you name the polygon with the same name as the net you want it to connect to, then you can just route a trace staring from anywhere within the polygon and Eagle will know they are meant to be connected.