I figured out how to do this. The below gives the general instructions. I am still learning.
First, establish a project.
http://docs.notepad-plus-plus.org/index.php/Project_Management.
Next, establish a directory tree in the Workspace/project.
folder_1
-> sub_folder_1
The directory tree folders have got to mirror (have the exact same structure as) the folders on the server.
Download the files from the NppFTP plugin.
The directory tree in the Workspace/project is automatically filled. Click on the Doc Switcher ta at the bottom. In the Doc Switcher area you can see which files have been saved/uploaded and which have not.
You can edit a file. When saved, the file automatically uploads to the server via the NppFTP plugin.