Well, it is true. In Eagle, rectangles have no name, so can't be linked to nets... If you want, you can draw everthing again with polygons, but there's no need. If you put a PCB trace over the rectangle, they will be linked by the copper. If you run the Desing Rules Check, it will indicate an 'overlap' error, but you can check it as 'approved', because this is your intention. Sometimes I need to use this trick, because in some cases it is faster than edit a component in a library, and the PCB manufacturers do not complain. They just care for the gerber files you generate. There's a file for each layer, and the file for the 'TOP' layer, in red, for example, will pick everything that's red. Doesn't matter if are single traces, nets, polygons, rectangles or texts.