You must always make sure your selection starts at the beginning of the first bar and goes all the way to the end of the last bar you want to change (including the last bar line).
Unzip this file to a new folder on your harddrive, for example C:\NoteWhizzy. In NoteWorthy Composer, add a new User Tool (Alt+F8, New...). For Name type "NoteWhizzy" and for Command type "c:\NoteWhizzy\NoteWhizzy.exe" (without the quotes).
To run NoteWhizzy, first make a selection of two or more bars (of which the first one is the example of how they all should be). Then press Alt+F8, select NoteWhizzy and click Run. When the NoteWhizzy application comes up, press Enter twice.