You can do it in the .aspx file:

    <DayPilot:DayPilotScheduler ID="DayPilotScheduler1" runat="server" 
        ....
        >
        <Separators>
            <DayPilot:Separator Color="green" Location="02/01/2008 12:00:00" />
            <DayPilot:Separator Color="green" Location="02/03/2008 12:00:00" />
            <DayPilot:Separator Color="red" Location="02/02/2008 00:00:00" />
        </Separators>
    </DayPilot:DayPilotScheduler>

You can also add it in the code behind:

    protected void Page_Load(object sender, EventArgs e)
    {
        DayPilotScheduler1.Separators.Add(DateTime.Today, Color.Red);
    }