So looks like AA will be back and be in charge of baseball while Shapiro is mostly the business guy for those who were wondering. Via Kiley McDaniel:
Blue Jays: There was some chatter when Shapiro was in talks to join Toronto as president that he could become the top baseball decision maker, which would then force GM Alex Anthopoulos to assess his market, as his contract is expiring after the year and he would be the top candidate on the market. I’ve been told by multiple sources that this isn’t the case and Shapiro will function in more of a business role, leaving the baseball to Anthopoulos. So, this isn’t really even a situation to monitor, I’m just taking a chance to tell Blue Jays fans to calm down.