Below are the steps I used to install Desktop Director for a XenApp 6.5
1. Followed these instructions to setup Desktop Directory
2. Followed this article to remove this error
4. Set the discover service name to Service.AutoDiscoveryAddressesXA rather then Service.AutoDiscoveryAddresses
3. Set the default domain on the website by editing line 213 of LogOn.aspx located in C:\inetpub\wwwroot\DesktopDirector\ to the following. Change domainname to be your domain.
<asp:TextBox ID="Domain" runat="server" Text="domainname" CssClass="text-box"></asp:TextBox>