Do you mean to register the Control so you can call it anywhere in your code???
By placing this line of code at the top of my page
<%@ Register Src="~/Controls/MyControl.ascx"TagName="myControl" TagPrefix="pp" %>
I can call the Control with
<pp:mycontrol id=""myControl1"" runat=""server"" xmlns:pp="#unknown" />
so for example you could have your default page like
<%@ Page Language="C#" AutoEventWireup="true"
CodeFile="Default.aspx.cs" Inherits="WEB.MyWebsite.UI._Default"
Title="My Website" MasterPageFile="~/Template.master" %>
<%@ Register Src="~/Controls/MyControl.ascx" TagName="myControl" TagPrefix="pp" %>
<asp:Content ID="MainContent" ContentPlaceHolderID="MainContent" runat="Server">
<pp:myControl ID="myControl1" runat="server" />
</asp:Content>
Is that what you meant?