WoW lot’s to unpack here, This sheet here has all you need to know for the connection.(bottom right)
several posts on connecting up the “SWDIO” or SWD method are on here give those a look at a minimum.
Once connected and viewable in the Atmel App. Then PlatformIO will have some programmer menu populated , pick it, click a break point and GO!
YMMV based on your skill level and New Hardware Adaptability. 
Are you able to compile in PLIO?
I have a link on here with it some what documented. I’m using a Jlink , doesn’t really matter IMO same need different automobiles.
PLIO .ini to this:
Check this link for PLIO and SAMD21
HTH
GL 
PJ 