Per the diagram, http://www.societyofrobots.com/images/sbs_avr_schematic.png
the LED goes between PD4 and VCC, so to turn the LED on you need to set PD4 low.
From the code (SoR_Utils.h):
PORT_OFF(PORTD, 4);//turn LED on
PORT_ON(PORTD, 4);//turn LED off
The function LED_on uses PORT_OFF which is:
#define PORT_ON( port_letter, number ) port_letter |= (1<<number)
#define PORT_OFF( port_letter, number ) port_letter &= ~(1<<number)
and results in PORTD pin 4 going low which should turn the LED on.
So, to turn the LED on, you would call LED_on.
I have not used the pony prog so no help on that.