@Xroads: you have to simply write into eagle's command line:
polygon Gnd (or GND or gnd - depends on the signal name)
and it will assign the name to the polygon you intend to draw after..
BTW -you may place the crystal underneath the 1284p (see the dil40 machine pin socket there are such "windows"), I did it with dil28 narrow socket as well - Unless you plan to change the crystal too often it saves a lot of space. As the heights is concerned it fits nice..