Bear with me here as it's been awhile sense I've ran sense on my phone so I may be a little rusty on the menu options, and also have the Evo 3d. But if you go into settings>software update see if there is an option to uncheck automatically check for updates. If your phone is on JB possibly look for a 3-dot menu within that section as well to see if there are more options.
Edit: Okay, I booted my Gingerbread stock based rom that I have dual booted and the option is as follows: settings>system updates>htc software update - uncheck the "scheduled check" box.
I can't guarantee it is the same on your phone or on newer software but I can only check what I have :/