Hi David and welcome to the QlikCommunity,
In the AccessPoint, for the time being, you always and only see QVW documents, regardless the folders they are.
But what you can do is to create different categories (metadata) so each document appears under a different section in the Category dropdown list in the AccessPoint portal. To do this, go to the QMC, Documents, User Documents, click on the QVW file, and on the right part go to the Document Information tab. Fill the "Or Type a New Category" with the corresponding value to each document.
Hope that helps.