I have one of those SAM D21 Xplained boards. I also have one of the (real, not dot org) Arduino Zero beta test boards.
The Atmel Xplained board does not work with the Arduino (unreleased) beta software. I didn't investigate why. I only gave it a quick try, to see if Zero was somehow different than SAM D21 Xplained. It is.
I haven't tried either with Atmel Studio. I did recently buy an Atmel-ICE, with the intention of giving Atmel Studio a try soon.
I have not tried Arduino.org's software yet, other than a quick look at 1.5.8.1 to confirm it does not have Zero support. One of the branches on their github does seem to have zero support, but I haven't gone to the trouble of building it.