Cutout a polygon from another in any layer in Eagle CAD part creation
Talk to your board house.  Don't assume you know the best way for them to handle this.

Basically you seem to be asking for a plated-thru milled hole.  The first answer is to avoid that.  If you really can't, the second answer is to ask the board house how to specify it.  There are different processes, and it depends when the plating is done relative to the routing.  This may require a additional routing step, which may cost extra.  Again, see the first answer.