I have a MasterPage (MyBoxx.Master) referencing 2 usercontrols :
<%@ Master Language=\"C#\" AutoEventWireup=\"true\" CodeFile=\"MyBoxx.master.cs\" Inherits=\"
Depending on how you have your User Control coded you may or may not be able to access all it's properties/methods when exposing it to the master page as a master page property..
Here is a solution that works:
In your master page you need to register your user control (.ascx) and place it on the master within the form tag.
Register the User Control
<%@ Register Src="~/Controls/MyUserControl.ascx" TagPrefix="uc" TagName="MyUserControl" %>
Add the User Control to the Master Page