Note: This question was asked a long time ago and you surely have figured out what you need to do. However, I will post my reply just in case it's helpful to somebody else.
I had the same question as you. Looking through search results, I came across a Mathworks site that answered it for me.
If, say, you have a 2 channel signal in an iddata structure, you can access the output channels by: y1 = data.y(:,1); y2 = data.y(:,2);
Now y1 and y2 are regular double arrays.