In your masterpage code, add a reference to the header and footer user controls:
<%@ Register Src="~/App/UserControls/MenuControls/HeaderControl.ascx" TagName="menu" TagPrefix="cc1" %>
<%@ Register Src="~/App/UserControls/MenuControls/FooterControl.ascx" TagName="footer" TagPrefix="cc1" %>
Then inside the body tag, add some code similar to this for your layout:
<form id="form1" runat="server">
<asp:ScriptManager ID="manScript" runat="server" ScriptMode="Release" EnableViewState="false" />
<cms:CMSPortalManager runat="server" ID="manPortal" EnableViewState="False" />
<cms:CMSPagePlaceholder runat="server" ID="pagePlaceHolder">
<LayoutTemplate>
<div class="page-wrapper" id="content" role="main">
<cc1:menu runat="server"></cc1:menu>
<asp:ContentPlaceHolder ID="main" runat="server"></asp:ContentPlaceHolder>
<cc1:footer runat="server"></cc1:footer>
</div>
</LayoutTemplate>
</cms:CMSPagePlaceholder>
</form>