I don't see Stewart getting the call to the big leagues again anytime soon, and even if he does, where would he play? I think the organization wants Ian to have a huge year down in AAA to force the club's hand with a decision about his future with the Rockies. He's off to a great start, and if he can keep it going he will force the issue at some point. I don't expect any midseason trades of either Stewart or Atkins, but in the offseason something could happen depending on Stewart's season in AAA and how a potential contract extension with Atkins would play out.
As for the second base question, I don't see it happening. Stewart really isn't built as a second baseman - it was experimented with in the spring but he didn't get a lot of time at the position and I don't think he'll be put back there.