a message to upgrade to el capitan keeps showing in the desktop

What is generating the message? Can you provide a screen shot?

this should be the only message to upgrade

Keep in mind if you do not include El Capitan in your account before September 20th you may no longer be eligible to legally obtain it from Apple. You only need to add it, not download or install it.

I assume you mean this:

Others have complained of this and suggested this solution: open the Mac App Store and click on 'Updates' at the top. When that opens you should see a banner across the top for El Capitan: control-click this and the click 'Hide update'.

Note that Sierra will be released in five days and will replace El Capitan in the Store, so you may have to do this again if you don't want to download it.