There are multiple ways to upload you files to the WebDesktop. The first of which is to
drag and drop the file from your local desktop to the WebDesktop (note that your file will be uploaded to the explorer window of the WebDesktop you drop it in).
The second is to
browse to the the explorer window you want to upload your file to and click "upload" in the explorer window toolbar. After that you will be prompted to select the file on your local hard drive.
Browser restrictions occur for multiple files. If you want to upload multiple files at once, just add them to a zip/7z/Gzip/Tar archive on your local hard drive and upload the compressed file to the WebDesktop. Once you have uploaded the archive you decompress it on the WebDesktop.
Uploading a Windows application to the WebDesktop won't allow you to run it on the WebDesktop (you need Appetizer for X.io to do that).