If you need your users to download more than one file, you will have to provide the files in a ZIP. There's really not a way around that. Uploading other files using FTP to the location that your webstore files are saved, will more than likely cause you problems.
You may want to look into creating a self-extracting ZIP. 7-Zip is a free utility that can create self-extracting archives (7-Zip calls them SFX). I know WinZip does it but you have to buy it. This will allow you to present a single file to your users without them needing to know how to "un-zip" the file.
I do suggest you remove all of the files and directories you manually uploaded to the WebStoreProductFiles directory.