When I downloaded scrivener, I somehow put it on my desktop instead of into a program file. How can I remedy this?

Most probably you are talking about the Scrivener installation file you downloaded from the Internet. Double-click the downloaded file, and Scrivener will install itself on the system just like any other Windows program. After a successful installation, it should create a Scrivener Application Shortcut on your Desktop and a Scrivener group/icon within your Start menu Applications. HTH.