You could add controls in three ways, programmatically, from the web.config or through the control uploader from edit page.
Adding controls programmatically is possible if you are inheriting IWebModule interface. Therefore you could define your controls from the Controls property.
You are already familiar with adding controls from the web.config. Anyway, I am referencing the syntax.
<add name="My User Control" section="Generic Controls" URL="~/YourUserControl.ascx" description="some descriptive text" overrideToolboxItem="False" />
<add name="Custom Control" section="Custom Controls" type="Namespace.ClassName, AssemblyName" overrideToolboxItem="False" />
Perhaps other way to add controls would be to change the database directly which I do not recommend you unless you know very well what you are doing.
the Telerik team