There is an option to register the templates of custom controls so that they can be edited through the UI. This blog posts explains the process: http://www.sitefinity.com/blogs/slavo-ingilizovs-blog/2012/09/21/making-your-widget-templates-editable-through-the-ui.
However if you are using user controls you will not be able to use this method. This approach works with custom controls. You can find more about different types of widgets (user controls vs. custom control) here: http://www.sitefinity.com/documentation/documentationarticles/developers-guide/sitefinity-essentials/controls.