this way you can set the selected value of checkbox
<asp:CheckBoxList ID="CheckBoxList1" runat="server">
<asp:ListItem Value="0">One</asp:ListItem>
<asp:ListItem Value="1">Two</asp:ListItem>
<asp:ListItem Value="2">Three</asp:ListItem>
<asp:ListItem Value="3">Four</asp:ListItem>
</asp:CheckBoxList>
CheckBoxList1.SelectedValue = "2";
where "2" should be the value which you want to select.
foreach (ListItem check in CheckBoxList1.Items)
{
if (check.Selected == true)
{
" Your Code"
}
}