Hi,
I suggest you use substructures to export each section of your model. You can create a selection set of what you want to export in the Revit model and save it. Then when you create the repository there are two options for you to select. “Use Revit Current Selection” and Use ISM Substructures” check both of them and give the substructure a name like the name of the building you are exporting. Here is a link to the new ism features on the BE Communities website. http://communities.bentley.com/products/structural/w/structural__wiki/12559.what-s-new-in-ism-4-0.aspx