Flash programming for a custom design with SAME70
Have a look at the schematic for the SAME70 Xplained PCB. The header marked "JTAG" contains the necessary signals for programming without the secondary CPU. 

However, as the fine print in the MCU manual mentions, JTAG functionality is only for factory testing, and the SW-DP is what you would use with something like the JLINK. Image below is from the eval board user manual. 



From the MCU datasheet: 


  The JTAGSEL pin is used to select the JTAG boundary scan when asserted at a high level. It integrates a permanent
  pulldown resistor of about 15 kΩ to GND, so that it can be left unconnected for normal operations.
  
  The JTAG Debug Port TDI, TDO, TMS and TCK is inactive. It is provided for Boundary Scan Manufacturing Test
  purpose only.