What issues are you facing? I can just Register the UC like normal and add the tag in the code for the master page.
<%@ Master Language="C#" AutoEventWireup="true" CodeFile="MasterPage.master.cs" Inherits="Master_MasterPage" %>
<%@ Register Src="~/UserControls/EmployeeSearch.ascx" TagPrefix="uc1" TagName="EmployeeSearch" %>
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head runat="server">
<title></title>
<asp:ContentPlaceHolder id="head" runat="server">
</asp:ContentPlaceHolder>
</head>
<body>
<form id="form1" runat="server">
<uc1:EmployeeSearch runat="server" ID="ucEmployeeSearch" />
<div>
<asp:ContentPlaceHolder id="ContentPlaceHolder1" runat="server">
</asp:ContentPlaceHolder>
</div>
</form>
</body>
</html>