EAGLE PCB, how to specify an out-of-board component?
Simply create a new device whose footprint (package) matches the pads you want to solder to on the PCB.

Your off-board transformer can be represented as a transformer-looking symbol on your schematic with pins connecting to components elsewhere on the schematic. But you can make its package drawing as just the necessary number of pads in a row. When you place the device in your schematic, it will manifest as just solder pads on the PCB layout.