"Currently, if a user tries to run your software it simply won't run, and the user has to know to go into system settings and manually give it permission."

No, you don't need to go into system settings. Just right-click on the app and select "Open" from the context menu. This brings up an are-you-sure dialog that gives you the option to go ahead and run the app. If you choose to run it, Gatekeeper marks it as trusted and won't bother you about it next time.