While reading a publication, click the "Add to favorites" button, then select the folder you want it to put to. The bookmarks in "Quick launch" folder will display in the top app bar. The ones in the "Pinned to start screen" folder will appear on the main page of the app next to the "Studies" section.

You can delete a folder or a bookmark by long tapping on a bookmark in the top app bar and clicking the Delete button.

Also, if you want to update a bookmark with a new place in a document or with another chapter, hold your finger (or right mouse click) on that bookmark and click "Set to current chapter". It is useful for conducting a Bible study - you can mark the place where you stopped.

See also
http://biblereader-jw.blogspot.com/2014/12/holding-your-finger-gesture-in-windows.html