Don, I do it a bit differently than you may need to, simply because I can copy files from my weather PC directly to my web server.
I created a batch file and run it every hour using a scheduler. It could be run daily as well, but I like to keep my file updated often. It looks at the noaa files and the first line copies any new file to my web server, and the second line copies any updated files.
REPLACE C:\master\vws\data\noaa\*.* "F:\weather\noaa" /A
REPLACE C:\master\vws\data\noaa\*.* "F:\weather\noaa" /U
I use a scheduling program called VisualCron that works like Windows Scheduler, but much better. My method would also work using WebDrive as an ftp option.
If you want to use the internal vws tools I guess you could modify the batch file to copy the updated files to an empty directory and then use the ftp Upload Folder menu choice to send the updated files from that folder. You could do it daily and make sure the batch file first deleted all files from the folder before it copies any updates.