How about adding a PNP transistor or something to the CHK signal of the MAX1555 and then make it available as a pin on the board.
That would allow the main device to know when the battery is charging, and keep itself on low power state.
Do you think the CHK can directly sink the current provided by an IO pin of an atmega for example?
If so, we could directly connect the IO to the ground side of the extra LED holes.
It might also be nice to have a male usb pinout connected internally to the usb socket, so that we could connect for example a FTDI usb to serial adapter and be able to use the same female usb socket for both charging and communication.