InCopy layout view?

[Norma5C5D]

Trying to implement InCopy but find when I export stories the page layout gets all jumbled. The main text boxes are now full page rather than smaller. The notes to the left of the main body (separate text box) are in the middle of the main text box, they need to stay in place and be editable .. is that possible? The main text box is a running text box story.

 

[BobLevine]

We need a full and detailed run down on your workflow including software and operating system rundowns.