Good morning Justin,
Jeff Atwood has a good article about emulating folders in the Amazon S3 service (Using Amazon S3 as an Image Hosting Service). So the way you'd do it is to create a download site URL that wyBuild understands. Something like this:
http://s3.amazonaws.com/your-account/updates/%file%
Then upload your files with the object names prepended with the "updates/" "folder" name. Like "updates/wyserver.wys", etc.
Does that make sense?