Does the Sparkfun SAMD21 Mini/Dev Breakout work with the ATMEL Studio
You need to go through the Atmel SAMD21 datasheet. I am currently using SWD pins for debugging an Atmel SAMD20 using Raspberry Pi3 which is running OpenOCD. You can use the same SWD pins to connect to an Atmel-ICE or Segger J-Link to program/debug.

You can use this as a reference: atsamd21-arduino SWD debugging