How are SMD thermal pads handled in Kicad's eeschema?
I don't know if there's other ways to do it, but the ground pad is going to end up being a pin of some sort. You could try drawing something in the module editor that suggests a pad, but in the end it comes down to pins. Make a pin on the schematic part and call it (the pin number) "PAD". Similarly, call/number the ground pad on the footprint "PAD". Then if you link PAD to ground on the schematic, the connection will get into the netlist. You also might want to add some text in the schematic about the thermal pad.