Evolphin Zoom is able to handle assets that are both individual assets and entire folders. In InDesign, layouts can encompass a variety of different images or other documents that are linked. Links that are contained within a sub-folder next to the INDD folder will perform a relative link. As a result, it is suggested that when possible to contain InDesign projects as a folder.
When checking out an InDesign document, it is suggested then to checkout the the containing folder. That way, all of the related assets could then be checked out at the same time.
When you are checking an InDesign document, it is then advised to Checkin parent directory.