I am looking into getting a Atomos Ninja 2. My Question is can I record audio through the Atomos, I ask this as my A6000 has no mic jack so it would be good it I could record the audio from the atomos itself.

The Ninja 2 has an unbalanced, stereo 1/8" audio input.

It can also take audio via the HDMI connection (but of course, if the cam has no audio, not a big deal)