I have added both the msi and setup.exe into the File & Folders tab.
I take it you want to update by distributing new MSIs rather than letting wyUpdate patch your files? If you are delivering your MSI and setup.exe as part of your update, then add them to the temporary folder in wyBuild and set the setup.exe to execute before your update.
In Download sites, I have added one site. Do we manuallly copy over the msi and exe from above to this folder or does wyBuild do that for us or is this the xxxx.wyu file thats generated?
I'm not quite sure what you mean. Add your setup.exe and msi to wyBuild (to the temp folder), then once you build your update it will output *.wys and *.wyu files. The *.wys and *.wyu contain all the files and information needed to execute the files.
Error trying to save file: Error downloading "http://localhost/Installers/wyserver.wys": The remote server returned an error: (404) Not Found.
Are you using IIS? If so make sure you set the MIME types of *.wys and *.wyu files as "application/octet-stream". See Why do I get a "404 not found error" when downloading wyserver.wys?.
Tell me if this helps.