You'll see the popup starts with...
*Popup !New !Popup
and ends with...
*Popup ~New

That defines the start and end of your main popup. Anything you want to add to the main popup needs to be within those two entries.

You'll notice there are entries that start with...
*Popup "somename" Folder
and ends with...
*Popup ~Folder

That defines the start and end of a folder within the popup. Entries within those will be inside of that folder of "somename". Folders can be inside of folders.

Naked entries that occur by themselves, and not within a folder, like...
*Popup "My C: Drive" !execute ["$FileManager$" "c:\"]
...will appear on the first page. They must be between the !New and ~New entries, though.

Oh ya, and RTFM. :)