The SWD interface of the SAM D20 is routed to the 10-pin JTAG connector and the 6-pin ISP connector of the STK600. The pinout is shown in the figure below, in addition to the pinout for the SAM-ICE.
Figure 1. Tool Pinout

It is necessary to use single wires to connect the SAM-ICE to the STK600 headers. The picture below is a reference for making the connections.
Figure 2. Connecting SAM-ICE over SWD