I know it is a very old post but I have seen many guys asking how to do this and the answer is simple.
Register that usercontrol in the host page and create a control too. Later from code behind use the control id to call a public method in user control.
<%@ Page Title="" Language="C#" AutoEventWireup="true" CodeFile="incidents.aspx.cs" Inherits="WebPages_incidents" %>
<%@ Register Src="~/UserControls/NewCargo.ascx" TagPrefix="uc1" TagName="NewCargo" %>
some html code
<uc1:NewCargo ID="newCargo1" runat="server" />
now in code behind
'newCargo1' is the control id of that usercontrol and 'showPopupNewCargo' is a public method in usercontrol.
Hope i was any helpful.